Starting phenix.real_space_refine on Sun Jul 5 02:26:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oz5_17298/07_2026/8oz5_17298_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oz5_17298/07_2026/8oz5_17298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oz5_17298/07_2026/8oz5_17298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oz5_17298/07_2026/8oz5_17298.map" model { file = "/net/cci-nas-00/data/ceres_data/8oz5_17298/07_2026/8oz5_17298_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oz5_17298/07_2026/8oz5_17298_trim.cif" } resolution = 2.04 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 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: 8 Type Number sf(0) Gaussians Ca 6 9.91 5 K 6 8.98 5 Fe 12 7.16 5 P 24 5.49 5 S 174 5.16 5 C 15708 2.51 5 N 4266 2.21 5 O 4798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24994 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4049 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 29, 'TRANS': 484} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 94 Ad-hoc single atom residues: {' FE': 2, ' K': 1, ' CA': 1} Unusual residues: {'BYN': 1, 'WC8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 4.17, per 1000 atoms: 0.17 Number of scatterers: 24994 At special positions: 0 Unit cell: (136.431, 148.149, 92.907, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 12 26.01 Ca 6 19.99 K 6 19.00 S 174 16.00 P 24 15.00 O 4798 8.00 N 4266 7.00 C 15708 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: 2.14 Conformation dependent library (CDL) restraints added in 904.0 milliseconds 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 132 helices and 30 sheets defined 38.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 118 through 122 removed outlier: 3.653A pdb=" N GLU A 122 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 162 Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 234 through 244 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 334 through 357 removed outlier: 4.856A pdb=" N VAL A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR A 371 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 Processing helix chain 'A' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 430 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 504 through 514 Processing helix chain 'A' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU B 122 " --> pdb=" O PRO B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 162 Processing helix chain 'B' and resid 188 through 197 Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 234 through 244 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 320 through 324 Processing helix chain 'B' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.694A pdb=" N THR B 371 " --> pdb=" O TYR B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 Processing helix chain 'B' and resid 389 through 402 removed outlier: 3.519A pdb=" N ASN B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 430 Processing helix chain 'B' and resid 450 through 455 Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 504 through 514 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.901A pdb=" N SER B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU C 122 " --> pdb=" O PRO C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.662A pdb=" N TRP C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 162 Processing helix chain 'C' and resid 188 through 197 Processing helix chain 'C' and resid 213 through 221 Processing helix chain 'C' and resid 234 through 244 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 320 through 324 Processing helix chain 'C' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR C 371 " --> pdb=" O TYR C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 Processing helix chain 'C' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN C 393 " --> pdb=" O GLY C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 430 Processing helix chain 'C' and resid 450 through 455 Processing helix chain 'C' and resid 456 through 458 No H-bonds generated for 'chain 'C' and resid 456 through 458' Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 504 through 514 Processing helix chain 'C' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER C 521 " --> pdb=" O GLY C 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 31 Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 80 through 89 Processing helix chain 'D' and resid 92 through 106 Processing helix chain 'D' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 162 Processing helix chain 'D' and resid 188 through 197 Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 234 through 244 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 320 through 324 Processing helix chain 'D' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL D 344 " --> pdb=" O ILE D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.694A pdb=" N THR D 371 " --> pdb=" O TYR D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 Processing helix chain 'D' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN D 393 " --> pdb=" O GLY D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 430 Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 456 through 458 No H-bonds generated for 'chain 'D' and resid 456 through 458' Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 517 through 526 removed outlier: 3.901A pdb=" N SER D 521 " --> pdb=" O GLY D 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 46 through 54 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 92 through 106 Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU E 122 " --> pdb=" O PRO E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.662A pdb=" N TRP E 134 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 162 Processing helix chain 'E' and resid 188 through 197 Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 234 through 244 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'E' and resid 334 through 357 removed outlier: 4.856A pdb=" N VAL E 344 " --> pdb=" O ILE E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR E 371 " --> pdb=" O TYR E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 Processing helix chain 'E' and resid 389 through 402 removed outlier: 3.520A pdb=" N ASN E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 430 Processing helix chain 'E' and resid 450 through 455 Processing helix chain 'E' and resid 456 through 458 No H-bonds generated for 'chain 'E' and resid 456 through 458' Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 504 through 514 Processing helix chain 'E' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER E 521 " --> pdb=" O GLY E 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 31 Processing helix chain 'F' and resid 46 through 54 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 92 through 106 Processing helix chain 'F' and resid 118 through 122 removed outlier: 3.654A pdb=" N GLU F 122 " --> pdb=" O PRO F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.661A pdb=" N TRP F 134 " --> pdb=" O ASP F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 162 Processing helix chain 'F' and resid 188 through 197 Processing helix chain 'F' and resid 213 through 221 Processing helix chain 'F' and resid 234 through 244 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 320 through 324 Processing helix chain 'F' and resid 334 through 357 removed outlier: 4.855A pdb=" N VAL F 344 " --> pdb=" O ILE F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 371 removed outlier: 3.695A pdb=" N THR F 371 " --> pdb=" O TYR F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 Processing helix chain 'F' and resid 389 through 402 removed outlier: 3.519A pdb=" N ASN F 393 " --> pdb=" O GLY F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 430 Processing helix chain 'F' and resid 450 through 455 Processing helix chain 'F' and resid 456 through 458 No H-bonds generated for 'chain 'F' and resid 456 through 458' Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 504 through 514 Processing helix chain 'F' and resid 517 through 526 removed outlier: 3.900A pdb=" N SER F 521 " --> pdb=" O GLY F 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL A 35 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG A 72 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL A 111 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS A 251 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA A 308 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG A 274 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 310 " --> pdb=" O HIS A 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU A 268 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE A 316 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 266 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL A 157 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 207 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN A 173 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN A 379 " --> pdb=" O GLN A 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 364 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE A 377 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 408 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA A 477 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA A 410 " --> pdb=" O ALA A 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL B 35 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG B 72 " --> pdb=" O ILE B 327 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL B 111 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS B 251 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA B 308 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ARG B 274 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 310 " --> pdb=" O HIS B 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU B 268 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE B 316 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 266 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 157 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 207 " --> pdb=" O CYS B 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN B 173 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 361 through 365 removed outlier: 6.648A pdb=" N GLN B 379 " --> pdb=" O GLN B 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL B 364 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 377 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 408 " --> pdb=" O ILE B 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA B 477 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 410 " --> pdb=" O ALA B 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL C 35 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG C 72 " --> pdb=" O ILE C 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL C 111 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS C 251 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA C 308 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG C 274 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 310 " --> pdb=" O HIS C 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU C 268 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 316 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL C 266 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 157 " --> pdb=" O PRO C 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 207 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN C 173 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN C 379 " --> pdb=" O GLN C 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL C 364 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 377 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA C 408 " --> pdb=" O ILE C 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA C 477 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA C 410 " --> pdb=" O ALA C 477 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL D 35 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG D 72 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 111 through 112 removed outlier: 6.428A pdb=" N VAL D 111 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N LYS D 251 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA D 308 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG D 274 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR D 310 " --> pdb=" O HIS D 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU D 268 " --> pdb=" O THR D 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE D 316 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 266 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL D 157 " --> pdb=" O PRO D 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 207 " --> pdb=" O CYS D 155 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN D 173 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN D 379 " --> pdb=" O GLN D 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL D 364 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 377 " --> pdb=" O VAL D 364 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA D 408 " --> pdb=" O ILE D 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA D 477 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA D 410 " --> pdb=" O ALA D 477 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL E 35 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG E 72 " --> pdb=" O ILE E 327 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 111 through 112 removed outlier: 6.429A pdb=" N VAL E 111 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS E 251 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 123 through 125 removed outlier: 8.950A pdb=" N ALA E 308 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ARG E 274 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR E 310 " --> pdb=" O HIS E 272 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLU E 268 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE E 316 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL E 266 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL E 157 " --> pdb=" O PRO E 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR E 207 " --> pdb=" O CYS E 155 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN E 173 " --> pdb=" O THR E 181 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 361 through 365 removed outlier: 6.648A pdb=" N GLN E 379 " --> pdb=" O GLN E 362 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL E 364 " --> pdb=" O ILE E 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE E 377 " --> pdb=" O VAL E 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA E 408 " --> pdb=" O ILE E 475 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ALA E 477 " --> pdb=" O ALA E 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA E 410 " --> pdb=" O ALA E 477 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.495A pdb=" N VAL F 35 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG F 72 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 111 through 112 removed outlier: 6.430A pdb=" N VAL F 111 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS F 251 " --> pdb=" O VAL F 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 123 through 125 removed outlier: 8.951A pdb=" N ALA F 308 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARG F 274 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR F 310 " --> pdb=" O HIS F 272 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLU F 268 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE F 316 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL F 266 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL F 157 " --> pdb=" O PRO F 205 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 207 " --> pdb=" O CYS F 155 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 123 through 125 removed outlier: 3.606A pdb=" N ASN F 173 " --> pdb=" O THR F 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 361 through 365 removed outlier: 6.647A pdb=" N GLN F 379 " --> pdb=" O GLN F 362 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL F 364 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE F 377 " --> pdb=" O VAL F 364 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA F 408 " --> pdb=" O ILE F 475 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA F 477 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA F 410 " --> pdb=" O ALA F 477 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2556 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: 5.19 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 4134 1.27 - 1.41: 6405 1.41 - 1.55: 14587 1.55 - 1.69: 86 1.69 - 1.82: 288 Bond restraints: 25500 Sorted by residual: bond pdb=" C ALA A 523 " pdb=" N ARG A 524 " ideal model delta sigma weight residual 1.334 1.644 -0.309 1.27e-02 6.20e+03 5.94e+02 bond pdb=" C ALA E 523 " pdb=" N ARG E 524 " ideal model delta sigma weight residual 1.334 1.644 -0.309 1.27e-02 6.20e+03 5.94e+02 bond pdb=" C ALA F 523 " pdb=" N ARG F 524 " ideal model delta sigma weight residual 1.334 1.644 -0.309 1.27e-02 6.20e+03 5.93e+02 bond pdb=" C ALA C 523 " pdb=" N ARG C 524 " ideal model delta sigma weight residual 1.334 1.643 -0.309 1.27e-02 6.20e+03 5.91e+02 bond pdb=" C ALA D 523 " pdb=" N ARG D 524 " ideal model delta sigma weight residual 1.334 1.643 -0.309 1.27e-02 6.20e+03 5.91e+02 ... (remaining 25495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.87: 34335 3.87 - 7.74: 251 7.74 - 11.61: 94 11.61 - 15.48: 12 15.48 - 19.35: 12 Bond angle restraints: 34704 Sorted by residual: angle pdb=" O4A WC8 A 602 " pdb=" P2A WC8 A 602 " pdb=" O5A WC8 A 602 " ideal model delta sigma weight residual 120.63 101.28 19.35 3.00e+00 1.11e-01 4.16e+01 angle pdb=" O4A WC8 D 602 " pdb=" P2A WC8 D 602 " pdb=" O5A WC8 D 602 " ideal model delta sigma weight residual 120.63 101.29 19.34 3.00e+00 1.11e-01 4.15e+01 angle pdb=" O4A WC8 B 602 " pdb=" P2A WC8 B 602 " pdb=" O5A WC8 B 602 " ideal model delta sigma weight residual 120.63 101.31 19.32 3.00e+00 1.11e-01 4.15e+01 angle pdb=" O4A WC8 F 602 " pdb=" P2A WC8 F 602 " pdb=" O5A WC8 F 602 " ideal model delta sigma weight residual 120.63 101.32 19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" O4A WC8 C 602 " pdb=" P2A WC8 C 602 " pdb=" O5A WC8 C 602 " ideal model delta sigma weight residual 120.63 101.33 19.30 3.00e+00 1.11e-01 4.14e+01 ... (remaining 34699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 14295 20.58 - 41.17: 861 41.17 - 61.75: 300 61.75 - 82.34: 18 82.34 - 102.92: 18 Dihedral angle restraints: 15492 sinusoidal: 6672 harmonic: 8820 Sorted by residual: dihedral pdb=" CA ARG B 489 " pdb=" C ARG B 489 " pdb=" N PRO B 490 " pdb=" CA PRO B 490 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA ARG C 489 " pdb=" C ARG C 489 " pdb=" N PRO C 490 " pdb=" CA PRO C 490 " ideal model delta harmonic sigma weight residual 180.00 -147.49 -32.51 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA ARG D 489 " pdb=" C ARG D 489 " pdb=" N PRO D 490 " pdb=" CA PRO D 490 " ideal model delta harmonic sigma weight residual -180.00 -147.50 -32.50 0 5.00e+00 4.00e-02 4.23e+01 ... (remaining 15489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.965: 3672 0.965 - 1.930: 0 1.930 - 2.895: 0 2.895 - 3.860: 0 3.860 - 4.825: 6 Chirality restraints: 3678 Sorted by residual: chirality pdb=" C20 BYN F 601 " pdb=" C19 BYN F 601 " pdb=" C21 BYN F 601 " pdb=" O5 BYN F 601 " both_signs ideal model delta sigma weight residual False -2.37 2.45 -4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C20 BYN C 601 " pdb=" C19 BYN C 601 " pdb=" C21 BYN C 601 " pdb=" O5 BYN C 601 " both_signs ideal model delta sigma weight residual False -2.37 2.45 -4.82 2.00e-01 2.50e+01 5.82e+02 chirality pdb=" C20 BYN E 601 " pdb=" C19 BYN E 601 " pdb=" C21 BYN E 601 " pdb=" O5 BYN E 601 " both_signs ideal model delta sigma weight residual False -2.37 2.45 -4.82 2.00e-01 2.50e+01 5.81e+02 ... (remaining 3675 not shown) Planarity restraints: 4470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BYN C 601 " -0.035 2.00e-02 2.50e+03 9.71e-02 2.59e+02 pdb=" C18 BYN C 601 " 0.103 2.00e-02 2.50e+03 pdb=" C2 BYN C 601 " 0.029 2.00e-02 2.50e+03 pdb=" C3 BYN C 601 " 0.070 2.00e-02 2.50e+03 pdb=" C4 BYN C 601 " 0.056 2.00e-02 2.50e+03 pdb=" C6 BYN C 601 " -0.251 2.00e-02 2.50e+03 pdb=" N1 BYN C 601 " -0.024 2.00e-02 2.50e+03 pdb=" N2 BYN C 601 " 0.005 2.00e-02 2.50e+03 pdb=" N4 BYN C 601 " 0.102 2.00e-02 2.50e+03 pdb=" O1 BYN C 601 " -0.088 2.00e-02 2.50e+03 pdb=" O3 BYN C 601 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BYN A 601 " 0.035 2.00e-02 2.50e+03 9.71e-02 2.59e+02 pdb=" C18 BYN A 601 " -0.103 2.00e-02 2.50e+03 pdb=" C2 BYN A 601 " -0.029 2.00e-02 2.50e+03 pdb=" C3 BYN A 601 " -0.070 2.00e-02 2.50e+03 pdb=" C4 BYN A 601 " -0.056 2.00e-02 2.50e+03 pdb=" C6 BYN A 601 " 0.251 2.00e-02 2.50e+03 pdb=" N1 BYN A 601 " 0.024 2.00e-02 2.50e+03 pdb=" N2 BYN A 601 " -0.004 2.00e-02 2.50e+03 pdb=" N4 BYN A 601 " -0.102 2.00e-02 2.50e+03 pdb=" O1 BYN A 601 " 0.088 2.00e-02 2.50e+03 pdb=" O3 BYN A 601 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BYN D 601 " -0.035 2.00e-02 2.50e+03 9.70e-02 2.59e+02 pdb=" C18 BYN D 601 " 0.103 2.00e-02 2.50e+03 pdb=" C2 BYN D 601 " 0.029 2.00e-02 2.50e+03 pdb=" C3 BYN D 601 " 0.069 2.00e-02 2.50e+03 pdb=" C4 BYN D 601 " 0.057 2.00e-02 2.50e+03 pdb=" C6 BYN D 601 " -0.251 2.00e-02 2.50e+03 pdb=" N1 BYN D 601 " -0.024 2.00e-02 2.50e+03 pdb=" N2 BYN D 601 " 0.004 2.00e-02 2.50e+03 pdb=" N4 BYN D 601 " 0.102 2.00e-02 2.50e+03 pdb=" O1 BYN D 601 " -0.089 2.00e-02 2.50e+03 pdb=" O3 BYN D 601 " 0.034 2.00e-02 2.50e+03 ... (remaining 4467 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.56: 276 2.56 - 3.21: 23612 3.21 - 3.85: 52351 3.85 - 4.50: 77442 4.50 - 5.14: 121438 Nonbonded interactions: 275119 Sorted by model distance: nonbonded pdb=" O9 BYN B 601 " pdb="FE FE B 603 " model vdw 1.920 3.000 nonbonded pdb=" O9 BYN F 601 " pdb="FE FE F 603 " model vdw 1.920 3.000 nonbonded pdb=" O9 BYN A 601 " pdb="FE FE A 603 " model vdw 1.920 3.000 nonbonded pdb=" O9 BYN E 601 " pdb="FE FE E 603 " model vdw 1.921 3.000 nonbonded pdb=" O9 BYN D 601 " pdb="FE FE D 603 " model vdw 1.921 3.000 ... (remaining 275114 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.880 Find NCS groups from input model: 0.300 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9162 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 : 0.011 0.309 25500 Z= 0.620 Angle : 1.012 19.350 34704 Z= 0.459 Chirality : 0.199 4.825 3678 Planarity : 0.005 0.097 4470 Dihedral : 15.008 102.923 9852 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.34 % Favored : 97.07 % Rotamer: Outliers : 2.08 % Allowed : 1.39 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3072 helix: -0.45 (0.15), residues: 996 sheet: -1.82 (0.22), residues: 486 loop : -1.12 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 175 TYR 0.010 0.001 TYR C 226 PHE 0.011 0.001 PHE A 449 TRP 0.005 0.001 TRP A 90 HIS 0.013 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.01101 / 0.62 (25500) covalent geometry : angle 1.01235 / 0.46 (34704) hydrogen bonds : bond 0.16736 / 11.04 ( 918) hydrogen bonds : angle 6.71841 / 4.78 ( 2556) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.095 Fit side-chains REVERT: A 511 MET cc_start: 0.8832 (mtp) cc_final: 0.8563 (mtm) REVERT: B 18 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6566 (tp30) REVERT: D 511 MET cc_start: 0.8860 (mtp) cc_final: 0.8597 (mtm) outliers start: 54 outliers final: 15 residues processed: 245 average time/residue: 0.7844 time to fit residues: 215.2975 Evaluate side-chains 188 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 151 SER Chi-restraints excluded: chain F residue 500 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 140 HIS A 183 GLN A 293 HIS A 295 HIS A 333 HIS A 393 ASN ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 293 HIS B 295 HIS B 333 HIS B 393 ASN ** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS C 293 HIS C 295 HIS C 393 ASN ** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 183 GLN D 293 HIS D 295 HIS D 393 ASN ** D 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS E 183 GLN E 293 HIS E 295 HIS E 393 ASN ** E 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS F 183 GLN F 293 HIS F 295 HIS F 393 ASN ** F 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.079945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.059458 restraints weight = 41240.431| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 1.96 r_work: 0.2568 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 25500 Z= 0.200 Angle : 0.653 7.790 34704 Z= 0.327 Chirality : 0.047 0.171 3678 Planarity : 0.004 0.030 4470 Dihedral : 12.078 103.987 4064 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.59 % Allowed : 2.80 % Favored : 96.61 % Rotamer: Outliers : 1.00 % Allowed : 5.05 % Favored : 93.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 3072 helix: 0.32 (0.16), residues: 1002 sheet: -1.52 (0.21), residues: 498 loop : -0.55 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 320 TYR 0.012 0.001 TYR F 218 PHE 0.017 0.001 PHE F 224 TRP 0.005 0.001 TRP F 518 HIS 0.006 0.002 HIS D 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (25500) covalent geometry : angle 0.65286 / 0.33 (34704) hydrogen bonds : bond 0.05966 / 3.86 ( 918) hydrogen bonds : angle 5.32531 / 3.79 ( 2556) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.945 Fit side-chains REVERT: B 491 VAL cc_start: 0.7443 (p) cc_final: 0.7226 (t) REVERT: C 491 VAL cc_start: 0.7429 (p) cc_final: 0.7203 (t) REVERT: D 147 MET cc_start: 0.9301 (mtm) cc_final: 0.9058 (mtt) REVERT: F 515 MET cc_start: 0.9062 (mtp) cc_final: 0.8813 (mtp) outliers start: 26 outliers final: 7 residues processed: 215 average time/residue: 0.6390 time to fit residues: 158.0327 Evaluate side-chains 176 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 169 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain F residue 151 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 9 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 97 optimal weight: 0.4980 chunk 216 optimal weight: 8.9990 chunk 271 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS ** B 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 HIS ** C 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS ** D 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS F 293 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.080385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.059882 restraints weight = 41309.932| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 1.96 r_work: 0.2580 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9292 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25500 Z= 0.178 Angle : 0.618 8.650 34704 Z= 0.311 Chirality : 0.047 0.236 3678 Planarity : 0.003 0.033 4470 Dihedral : 11.229 118.636 4043 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.09 % Favored : 96.39 % Rotamer: Outliers : 1.00 % Allowed : 5.25 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.15), residues: 3072 helix: 0.62 (0.17), residues: 1002 sheet: -1.10 (0.21), residues: 528 loop : -0.36 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 320 TYR 0.013 0.001 TYR A 218 PHE 0.014 0.001 PHE F 224 TRP 0.006 0.001 TRP A 373 HIS 0.010 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (25500) covalent geometry : angle 0.61845 / 0.31 (34704) hydrogen bonds : bond 0.05367 / 3.47 ( 918) hydrogen bonds : angle 5.00994 / 3.58 ( 2556) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.817 Fit side-chains REVERT: A 302 MET cc_start: 0.8915 (tpt) cc_final: 0.8689 (mmm) REVERT: C 202 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8801 (pm20) REVERT: C 302 MET cc_start: 0.8898 (tpt) cc_final: 0.8659 (tpt) REVERT: D 302 MET cc_start: 0.8944 (tpt) cc_final: 0.8686 (mmm) REVERT: E 302 MET cc_start: 0.8916 (tpt) cc_final: 0.8705 (mmm) REVERT: F 450 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8807 (mmt) REVERT: F 453 GLU cc_start: 0.7974 (tt0) cc_final: 0.7438 (mt-10) REVERT: F 515 MET cc_start: 0.9096 (mtp) cc_final: 0.8815 (mtp) outliers start: 26 outliers final: 8 residues processed: 197 average time/residue: 0.6218 time to fit residues: 140.2848 Evaluate side-chains 182 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 166 HIS Chi-restraints excluded: chain F residue 450 MET Chi-restraints excluded: chain F residue 473 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 203 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 296 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 293 HIS ** A 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 HIS B 357 GLN C 293 HIS C 357 GLN D 293 HIS D 357 GLN ** D 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS F 293 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.078890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.058100 restraints weight = 41301.414| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 1.98 r_work: 0.2547 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2433 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9303 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 25500 Z= 0.242 Angle : 0.635 7.796 34704 Z= 0.327 Chirality : 0.048 0.325 3678 Planarity : 0.004 0.033 4470 Dihedral : 11.356 135.715 4038 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.48 % Favored : 96.09 % Rotamer: Outliers : 1.58 % Allowed : 5.36 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.30 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3072 helix: 0.76 (0.17), residues: 996 sheet: -0.98 (0.22), residues: 528 loop : -0.27 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 527 TYR 0.014 0.002 TYR D 218 PHE 0.018 0.001 PHE F 224 TRP 0.008 0.001 TRP C 373 HIS 0.011 0.002 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.24 (25500) covalent geometry : angle 0.63512 / 0.33 (34704) hydrogen bonds : bond 0.05858 / 3.78 ( 918) hydrogen bonds : angle 5.00194 / 3.57 ( 2556) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.849 Fit side-chains REVERT: A 302 MET cc_start: 0.8986 (tpt) cc_final: 0.8723 (mmm) REVERT: D 302 MET cc_start: 0.9002 (tpt) cc_final: 0.8756 (mmm) REVERT: E 422 ASP cc_start: 0.9414 (OUTLIER) cc_final: 0.9150 (t0) REVERT: F 422 ASP cc_start: 0.9393 (OUTLIER) cc_final: 0.9124 (t0) REVERT: F 453 GLU cc_start: 0.8006 (tt0) cc_final: 0.7471 (mt-10) REVERT: F 515 MET cc_start: 0.9152 (mtp) cc_final: 0.8892 (mtp) outliers start: 41 outliers final: 14 residues processed: 209 average time/residue: 0.6522 time to fit residues: 156.4561 Evaluate side-chains 192 residues out of total 2592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 176 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 166 HIS Chi-restraints excluded: chain E residue 372 ASP Chi-restraints excluded: chain E residue 422 ASP Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 422 ASP Chi-restraints excluded: chain F residue 473 MET Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8392 > 50: distance: 64 - 66: 35.063 distance: 66 - 67: 20.039 distance: 67 - 68: 27.164 distance: 67 - 70: 37.544 distance: 68 - 69: 25.360 distance: 68 - 78: 33.205 distance: 70 - 71: 24.073 distance: 71 - 72: 32.940 distance: 71 - 73: 23.278 distance: 72 - 74: 43.436 distance: 73 - 75: 40.666 distance: 74 - 76: 15.348 distance: 75 - 76: 6.182 distance: 76 - 77: 6.251 distance: 78 - 79: 43.715 distance: 79 - 80: 49.916 distance: 79 - 82: 41.535 distance: 80 - 86: 68.629 distance: 82 - 83: 46.493 distance: 83 - 84: 36.082 distance: 83 - 85: 41.254 distance: 86 - 87: 39.842 distance: 87 - 88: 40.462 distance: 87 - 90: 36.104 distance: 88 - 89: 41.189 distance: 88 - 93: 41.940 distance: 90 - 91: 45.504 distance: 90 - 92: 40.203 distance: 93 - 94: 50.909 distance: 94 - 95: 41.834 distance: 94 - 97: 57.143 distance: 95 - 96: 37.925 distance: 95 - 102: 17.577 distance: 97 - 98: 56.894 distance: 98 - 99: 65.857 distance: 99 - 100: 5.363 distance: 99 - 101: 41.365 distance: 102 - 103: 20.770 distance: 103 - 104: 22.969 distance: 103 - 106: 27.215 distance: 104 - 105: 17.878 distance: 106 - 107: 57.195 distance: 106 - 108: 22.228 distance: 109 - 110: 42.196 distance: 110 - 111: 39.010 distance: 110 - 113: 8.199 distance: 111 - 112: 40.446 distance: 111 - 117: 41.429 distance: 113 - 114: 7.409 distance: 114 - 115: 36.697 distance: 114 - 116: 9.555 distance: 117 - 118: 19.411 distance: 118 - 119: 43.557 distance: 118 - 121: 48.809 distance: 119 - 120: 28.535 distance: 119 - 126: 10.629 distance: 121 - 122: 26.290 distance: 122 - 123: 14.201 distance: 123 - 124: 17.414 distance: 124 - 125: 36.164 distance: 126 - 127: 34.212 distance: 127 - 128: 41.471 distance: 128 - 129: 11.179 distance: 128 - 135: 48.972 distance: 130 - 131: 45.183 distance: 131 - 132: 40.177 distance: 132 - 133: 52.846 distance: 132 - 134: 27.427 distance: 135 - 136: 61.094 distance: 136 - 137: 44.558 distance: 136 - 139: 24.501 distance: 137 - 138: 39.592 distance: 139 - 140: 48.244 distance: 139 - 141: 42.171 distance: 142 - 143: 30.624 distance: 143 - 144: 30.121 distance: 143 - 146: 28.514 distance: 144 - 145: 40.563 distance: 144 - 150: 34.742 distance: 146 - 147: 40.478 distance: 147 - 149: 39.767