Starting phenix.real_space_refine on Fri Sep 27 17:45:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsb_29418/09_2024/8fsb_29418.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsb_29418/09_2024/8fsb_29418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsb_29418/09_2024/8fsb_29418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsb_29418/09_2024/8fsb_29418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsb_29418/09_2024/8fsb_29418.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fsb_29418/09_2024/8fsb_29418.cif" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 10950 2.51 5 N 2700 2.21 5 O 2945 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16640 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "B" Number of atoms: 3273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3273 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 20, 'TRANS': 374} Chain breaks: 1 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAG': 3, 'SRO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {'NAG': 3, 'SRO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: C, D, E Time building chain proxies: 9.17, per 1000 atoms: 0.55 Number of scatterers: 16640 At special positions: 0 Unit cell: (97.9, 97.9, 171.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 2945 8.00 N 2700 7.00 C 10950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 82 " " NAG A 502 " - " ASN A 148 " " NAG A 503 " - " ASN A 164 " " NAG B 502 " - " ASN B 82 " " NAG B 503 " - " ASN B 148 " " NAG B 504 " - " ASN B 164 " " NAG C 502 " - " ASN C 82 " " NAG C 503 " - " ASN C 148 " " NAG C 504 " - " ASN C 164 " " NAG D 502 " - " ASN D 82 " " NAG D 503 " - " ASN D 148 " " NAG D 504 " - " ASN D 164 " " NAG E 502 " - " ASN E 82 " " NAG E 503 " - " ASN E 148 " " NAG E 504 " - " ASN E 164 " Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 10 sheets defined 48.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 10 through 21 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP A 81 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.532A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 233 removed outlier: 4.978A pdb=" N LEU A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU A 266 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 308 removed outlier: 3.508A pdb=" N VAL A 285 " --> pdb=" O PRO A 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 411 through 418 Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP A 434 " --> pdb=" O GLY A 430 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 436 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU A 465 " --> pdb=" O SER A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP B 81 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 141 through 144 Processing helix chain 'B' and resid 170 through 176 removed outlier: 3.533A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 233 removed outlier: 4.978A pdb=" N LEU B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 233 through 243 removed outlier: 3.985A pdb=" N CYS B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU B 266 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 308 removed outlier: 3.509A pdb=" N VAL B 285 " --> pdb=" O PRO B 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP B 327 " --> pdb=" O HIS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 Processing helix chain 'B' and resid 398 through 410 Processing helix chain 'B' and resid 411 through 418 Processing helix chain 'B' and resid 419 through 424 Processing helix chain 'B' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 436 " --> pdb=" O VAL B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU B 465 " --> pdb=" O SER B 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'C' and resid 10 through 21 Processing helix chain 'C' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP C 81 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.532A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 233 removed outlier: 4.978A pdb=" N LEU C 229 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU C 266 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 308 removed outlier: 3.509A pdb=" N VAL C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP C 327 " --> pdb=" O HIS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 332 Processing helix chain 'C' and resid 398 through 410 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 419 through 424 Processing helix chain 'C' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU C 433 " --> pdb=" O VAL C 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP C 434 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 436 " --> pdb=" O VAL C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU C 465 " --> pdb=" O SER C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'D' and resid 10 through 21 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.906A pdb=" N ASP D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 141 through 144 Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.533A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 233 removed outlier: 4.977A pdb=" N LEU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 270 removed outlier: 3.654A pdb=" N LEU D 266 " --> pdb=" O TYR D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 308 removed outlier: 3.508A pdb=" N VAL D 285 " --> pdb=" O PRO D 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 308 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 327 removed outlier: 4.549A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP D 327 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 Processing helix chain 'D' and resid 398 through 410 Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU D 433 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP D 434 " --> pdb=" O GLY D 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 436 " --> pdb=" O VAL D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU D 465 " --> pdb=" O SER D 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'E' and resid 10 through 21 Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.905A pdb=" N ASP E 81 " --> pdb=" O GLU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 93 Processing helix chain 'E' and resid 141 through 144 Processing helix chain 'E' and resid 170 through 176 removed outlier: 3.532A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 233 removed outlier: 4.977A pdb=" N LEU E 229 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 233 through 243 removed outlier: 3.984A pdb=" N CYS E 243 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 270 removed outlier: 3.655A pdb=" N LEU E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 308 removed outlier: 3.507A pdb=" N VAL E 285 " --> pdb=" O PRO E 281 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL E 308 " --> pdb=" O ILE E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 327 removed outlier: 4.548A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP E 327 " --> pdb=" O HIS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 398 through 410 Processing helix chain 'E' and resid 411 through 418 Processing helix chain 'E' and resid 419 through 424 Processing helix chain 'E' and resid 426 through 461 removed outlier: 4.280A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASP E 434 " --> pdb=" O GLY E 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU E 436 " --> pdb=" O VAL E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 465 removed outlier: 3.906A pdb=" N LEU E 465 " --> pdb=" O SER E 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 462 through 465' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 7.149A pdb=" N TYR A 61 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE A 48 " --> pdb=" O TYR A 61 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TRP A 63 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR A 46 " --> pdb=" O TRP A 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG A 65 " --> pdb=" O ILE A 44 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE A 44 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR A 67 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASP A 42 " --> pdb=" O TYR A 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR A 69 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER A 40 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.551A pdb=" N ILE A 216 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 87 through 88 removed outlier: 7.149A pdb=" N TYR B 61 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE B 48 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TRP B 63 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR B 46 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG B 65 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE B 44 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR B 67 " --> pdb=" O ASP B 42 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASP B 42 " --> pdb=" O TYR B 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR B 69 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER B 40 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.551A pdb=" N ILE B 216 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 88 removed outlier: 7.150A pdb=" N TYR C 61 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ILE C 48 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N TRP C 63 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR C 46 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG C 65 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE C 44 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TYR C 67 " --> pdb=" O ASP C 42 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASP C 42 " --> pdb=" O TYR C 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR C 69 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N SER C 40 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.550A pdb=" N ILE C 216 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 87 through 88 removed outlier: 7.150A pdb=" N TYR D 61 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE D 48 " --> pdb=" O TYR D 61 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TRP D 63 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR D 46 " --> pdb=" O TRP D 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG D 65 " --> pdb=" O ILE D 44 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ILE D 44 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR D 67 " --> pdb=" O ASP D 42 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ASP D 42 " --> pdb=" O TYR D 67 " (cutoff:3.500A) removed outlier: 9.109A pdb=" N THR D 69 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N SER D 40 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.552A pdb=" N ILE D 216 " --> pdb=" O GLN D 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 87 through 88 removed outlier: 7.149A pdb=" N TYR E 61 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ILE E 48 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N TRP E 63 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N TYR E 46 " --> pdb=" O TRP E 63 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ARG E 65 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ILE E 44 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR E 67 " --> pdb=" O ASP E 42 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASP E 42 " --> pdb=" O TYR E 67 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N THR E 69 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N SER E 40 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.551A pdb=" N ILE E 216 " --> pdb=" O GLN E 147 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2190 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: 5.15 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4698 1.34 - 1.45: 2904 1.45 - 1.57: 9423 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 17095 Sorted by residual: bond pdb=" C LEU D 244 " pdb=" N PRO D 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.28e+01 bond pdb=" C LEU E 244 " pdb=" N PRO E 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" C LEU A 244 " pdb=" N PRO A 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" C LEU B 244 " pdb=" N PRO B 245 " ideal model delta sigma weight residual 1.329 1.371 -0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C LEU C 244 " pdb=" N PRO C 245 " ideal model delta sigma weight residual 1.329 1.370 -0.041 1.18e-02 7.18e+03 1.21e+01 ... (remaining 17090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 22534 1.69 - 3.38: 692 3.38 - 5.07: 99 5.07 - 6.76: 10 6.76 - 8.45: 20 Bond angle restraints: 23355 Sorted by residual: angle pdb=" N MET B 419 " pdb=" CA MET B 419 " pdb=" C MET B 419 " ideal model delta sigma weight residual 113.18 107.52 5.66 1.33e+00 5.65e-01 1.81e+01 angle pdb=" N MET A 419 " pdb=" CA MET A 419 " pdb=" C MET A 419 " ideal model delta sigma weight residual 113.18 107.56 5.62 1.33e+00 5.65e-01 1.79e+01 angle pdb=" N MET D 419 " pdb=" CA MET D 419 " pdb=" C MET D 419 " ideal model delta sigma weight residual 113.18 107.57 5.61 1.33e+00 5.65e-01 1.78e+01 angle pdb=" N MET E 419 " pdb=" CA MET E 419 " pdb=" C MET E 419 " ideal model delta sigma weight residual 113.18 107.58 5.60 1.33e+00 5.65e-01 1.77e+01 angle pdb=" N MET C 419 " pdb=" CA MET C 419 " pdb=" C MET C 419 " ideal model delta sigma weight residual 113.18 107.60 5.58 1.33e+00 5.65e-01 1.76e+01 ... (remaining 23350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 9002 15.06 - 30.12: 907 30.12 - 45.18: 247 45.18 - 60.24: 50 60.24 - 75.30: 35 Dihedral angle restraints: 10241 sinusoidal: 4346 harmonic: 5895 Sorted by residual: dihedral pdb=" CA ASP E 425 " pdb=" C ASP E 425 " pdb=" N TRP E 426 " pdb=" CA TRP E 426 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP D 425 " pdb=" C ASP D 425 " pdb=" N TRP D 426 " pdb=" CA TRP D 426 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP A 425 " pdb=" C ASP A 425 " pdb=" N TRP A 426 " pdb=" CA TRP A 426 " ideal model delta harmonic sigma weight residual 180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 10238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1889 0.044 - 0.088: 623 0.088 - 0.132: 203 0.132 - 0.176: 15 0.176 - 0.220: 10 Chirality restraints: 2740 Sorted by residual: chirality pdb=" CA PHE E 142 " pdb=" N PHE E 142 " pdb=" C PHE E 142 " pdb=" CB PHE E 142 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE A 142 " pdb=" N PHE A 142 " pdb=" C PHE A 142 " pdb=" CB PHE A 142 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA PHE B 142 " pdb=" N PHE B 142 " pdb=" C PHE B 142 " pdb=" CB PHE B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2737 not shown) Planarity restraints: 2860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 81 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" C ASP A 81 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP A 81 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN A 82 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 81 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ASP D 81 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP D 81 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN D 82 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 81 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.10e+00 pdb=" C ASP E 81 " -0.035 2.00e-02 2.50e+03 pdb=" O ASP E 81 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN E 82 " 0.012 2.00e-02 2.50e+03 ... (remaining 2857 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 74 2.60 - 3.18: 13418 3.18 - 3.75: 24594 3.75 - 4.33: 33411 4.33 - 4.90: 55193 Nonbonded interactions: 126690 Sorted by model distance: nonbonded pdb=" SG CYS E 135 " pdb=" SG CYS E 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS D 135 " pdb=" SG CYS D 149 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS C 135 " pdb=" SG CYS C 149 " model vdw 2.032 3.760 nonbonded pdb=" OD1 ASN E 148 " pdb=" N2 NAG E 503 " model vdw 2.376 3.120 nonbonded pdb=" OD1 ASN C 148 " pdb=" N2 NAG C 503 " model vdw 2.376 3.120 ... (remaining 126685 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'B' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'C' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'D' and (resid 7 through 465 or resid 502 through 503)) selection = (chain 'E' and (resid 7 through 465 or resid 502 through 503)) } 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: 1.510 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.900 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.004 0.054 17095 Z= 0.252 Angle : 0.714 8.454 23355 Z= 0.382 Chirality : 0.048 0.220 2740 Planarity : 0.004 0.031 2845 Dihedral : 14.088 75.300 6395 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 1955 helix: 0.60 (0.19), residues: 745 sheet: -0.43 (0.26), residues: 395 loop : -1.65 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 168 HIS 0.002 0.001 HIS C 18 PHE 0.021 0.002 PHE E 303 TYR 0.015 0.002 TYR D 61 ARG 0.007 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.943 Fit side-chains revert: symmetry clash REVERT: A 410 ARG cc_start: 0.7560 (ttp-170) cc_final: 0.7237 (tpm-80) REVERT: A 411 HIS cc_start: 0.7745 (m90) cc_final: 0.7528 (m-70) REVERT: B 410 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7425 (tpt90) REVERT: B 411 HIS cc_start: 0.7759 (m90) cc_final: 0.7485 (m-70) REVERT: C 411 HIS cc_start: 0.7722 (m90) cc_final: 0.7504 (m-70) REVERT: C 419 MET cc_start: 0.5392 (mmt) cc_final: 0.5163 (tmm) REVERT: D 410 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7533 (tpt90) REVERT: D 411 HIS cc_start: 0.7490 (m90) cc_final: 0.7156 (m90) REVERT: E 416 ARG cc_start: 0.6574 (ttt180) cc_final: 0.5786 (tpm170) REVERT: E 419 MET cc_start: 0.5515 (mmt) cc_final: 0.5246 (tmm) outliers start: 0 outliers final: 1 residues processed: 213 average time/residue: 1.2454 time to fit residues: 295.6643 Evaluate side-chains 90 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 89 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 442 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 50 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 161 GLN C 9 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17095 Z= 0.182 Angle : 0.576 7.376 23355 Z= 0.298 Chirality : 0.043 0.167 2740 Planarity : 0.004 0.029 2845 Dihedral : 7.078 58.007 2507 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.90 % Allowed : 9.21 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1955 helix: 0.83 (0.19), residues: 790 sheet: -0.50 (0.26), residues: 395 loop : -1.67 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 168 HIS 0.002 0.000 HIS C 119 PHE 0.012 0.001 PHE A 142 TYR 0.013 0.001 TYR B 61 ARG 0.005 0.000 ARG B 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 97 time to evaluate : 1.746 Fit side-chains REVERT: A 410 ARG cc_start: 0.7606 (ttp-170) cc_final: 0.7232 (tpm-80) REVERT: A 411 HIS cc_start: 0.7824 (m90) cc_final: 0.7589 (m-70) REVERT: B 410 ARG cc_start: 0.7639 (ttp-170) cc_final: 0.7350 (tpt90) REVERT: B 411 HIS cc_start: 0.7751 (m90) cc_final: 0.7442 (m-70) REVERT: D 410 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7392 (tpt90) REVERT: D 411 HIS cc_start: 0.7476 (m90) cc_final: 0.7078 (m90) REVERT: E 416 ARG cc_start: 0.6362 (ttt180) cc_final: 0.5990 (tpm170) outliers start: 35 outliers final: 13 residues processed: 127 average time/residue: 0.9420 time to fit residues: 139.4511 Evaluate side-chains 94 residues out of total 1845 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 303 PHE Chi-restraints excluded: chain A residue 440 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 440 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4697 > 50: distance: 77 - 207: 25.150 distance: 87 - 210: 8.461 distance: 131 - 135: 10.386 distance: 135 - 136: 17.935 distance: 136 - 137: 24.135 distance: 136 - 139: 13.459 distance: 137 - 138: 22.903 distance: 137 - 149: 38.722 distance: 139 - 140: 13.346 distance: 140 - 141: 21.431 distance: 140 - 142: 14.416 distance: 141 - 143: 15.933 distance: 142 - 144: 21.994 distance: 142 - 145: 8.651 distance: 143 - 144: 3.239 distance: 144 - 146: 5.996 distance: 145 - 147: 20.979 distance: 146 - 148: 6.737 distance: 147 - 148: 14.193 distance: 149 - 150: 15.821 distance: 150 - 151: 20.441 distance: 150 - 153: 5.280 distance: 151 - 152: 13.570 distance: 151 - 157: 18.325 distance: 153 - 154: 3.657 distance: 154 - 155: 31.626 distance: 154 - 156: 34.737 distance: 157 - 158: 12.473 distance: 158 - 159: 12.262 distance: 158 - 161: 19.946 distance: 159 - 160: 24.468 distance: 159 - 167: 19.430 distance: 161 - 162: 12.275 distance: 162 - 163: 25.349 distance: 162 - 164: 18.767 distance: 163 - 165: 12.782 distance: 164 - 166: 6.001 distance: 165 - 166: 11.943 distance: 167 - 168: 7.520 distance: 168 - 169: 3.451 distance: 168 - 171: 10.942 distance: 169 - 170: 28.916 distance: 169 - 174: 22.619 distance: 171 - 172: 30.056 distance: 171 - 173: 4.502 distance: 174 - 175: 18.174 distance: 175 - 176: 18.573 distance: 175 - 178: 14.666 distance: 176 - 177: 14.539 distance: 176 - 182: 6.895 distance: 178 - 179: 6.884 distance: 178 - 180: 15.743 distance: 179 - 181: 23.393 distance: 182 - 183: 12.503 distance: 183 - 184: 8.516 distance: 183 - 186: 22.339 distance: 184 - 185: 11.478 distance: 184 - 191: 5.199 distance: 186 - 187: 17.201 distance: 187 - 188: 18.607 distance: 188 - 189: 17.111 distance: 188 - 190: 14.160 distance: 191 - 192: 15.696 distance: 192 - 193: 9.547 distance: 192 - 195: 27.197 distance: 193 - 194: 16.928 distance: 193 - 199: 7.755 distance: 195 - 196: 4.460 distance: 196 - 197: 26.514 distance: 196 - 198: 4.486 distance: 199 - 200: 6.245 distance: 200 - 201: 12.249 distance: 200 - 203: 5.078 distance: 201 - 202: 4.493 distance: 201 - 207: 20.906 distance: 203 - 204: 31.134 distance: 203 - 205: 17.466 distance: 204 - 206: 20.796 distance: 207 - 208: 13.677 distance: 208 - 209: 9.386 distance: 208 - 211: 22.347 distance: 209 - 210: 5.245 distance: 209 - 215: 9.801 distance: 211 - 212: 11.511 distance: 212 - 213: 19.104 distance: 212 - 214: 17.474 distance: 214 - 278: 26.870 distance: 215 - 216: 18.233 distance: 216 - 217: 19.735 distance: 216 - 219: 4.978 distance: 217 - 218: 33.394 distance: 217 - 223: 10.865 distance: 219 - 220: 12.786 distance: 219 - 221: 29.710 distance: 220 - 222: 18.259