Starting phenix.real_space_refine on Fri Sep 27 03:09:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc7_42116/09_2024/8uc7_42116_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc7_42116/09_2024/8uc7_42116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc7_42116/09_2024/8uc7_42116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc7_42116/09_2024/8uc7_42116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc7_42116/09_2024/8uc7_42116_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uc7_42116/09_2024/8uc7_42116_neut.cif" } resolution = 2.9 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 108 5.16 5 C 9748 2.51 5 N 2456 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14840 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3633 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 170 Chain: "A" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Unusual residues: {'PCW': 3, 'PFL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 23 Restraints were copied for chains: C, B, D Time building chain proxies: 8.17, per 1000 atoms: 0.55 Number of scatterers: 14840 At special positions: 0 Unit cell: (114.915, 114.915, 115.73, 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 108 16.00 O 2528 8.00 N 2456 7.00 C 9748 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: 3.84 Conformation dependent library (CDL) restraints added in 2.0 seconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 73.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.680A pdb=" N ARG D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Proline residue: D 161 - end of helix removed outlier: 3.901A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.808A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 removed outlier: 3.807A pdb=" N LYS D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER D 228 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.293A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 4.504A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.748A pdb=" N VAL D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.578A pdb=" N GLU D 452 " --> pdb=" O ASN D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 471 removed outlier: 5.550A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 4.077A pdb=" N ALA D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 543 Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 586 removed outlier: 3.985A pdb=" N VAL D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN A 103 " --> pdb=" O SER A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.681A pdb=" N ARG A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.901A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.808A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.806A pdb=" N LYS A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.293A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 4.505A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.748A pdb=" N VAL A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.577A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 removed outlier: 5.550A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 4.077A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.984A pdb=" N VAL A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.680A pdb=" N ARG B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.901A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.808A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.808A pdb=" N LYS B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.294A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 4.505A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.748A pdb=" N VAL B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.578A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 removed outlier: 5.550A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 4.077A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 586 removed outlier: 3.985A pdb=" N VAL B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.680A pdb=" N ARG C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Proline residue: C 161 - end of helix removed outlier: 3.901A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.809A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.807A pdb=" N LYS C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.292A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 4.504A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.747A pdb=" N VAL C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.578A pdb=" N GLU C 452 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 471 removed outlier: 5.549A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 4.076A pdb=" N ALA C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 586 removed outlier: 3.985A pdb=" N VAL C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.627A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.698A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.627A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.699A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.626A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.698A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.627A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.698A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2931 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: 4.92 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2296 1.27 - 1.41: 4126 1.41 - 1.54: 8379 1.54 - 1.68: 203 1.68 - 1.81: 188 Bond restraints: 15192 Sorted by residual: bond pdb=" C19 PCW C 704 " pdb=" C20 PCW C 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C19 PCW B 704 " pdb=" C20 PCW B 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C19 PCW A 704 " pdb=" C20 PCW A 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C19 PCW D 704 " pdb=" C20 PCW D 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C18 PCW B 704 " pdb=" C19 PCW B 704 " ideal model delta sigma weight residual 1.497 1.333 0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 15187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 16949 2.30 - 4.60: 3443 4.60 - 6.90: 143 6.90 - 9.21: 21 9.21 - 11.51: 24 Bond angle restraints: 20580 Sorted by residual: angle pdb=" N TYR C 513 " pdb=" CA TYR C 513 " pdb=" C TYR C 513 " ideal model delta sigma weight residual 109.52 121.03 -11.51 1.55e+00 4.16e-01 5.51e+01 angle pdb=" N TYR D 513 " pdb=" CA TYR D 513 " pdb=" C TYR D 513 " ideal model delta sigma weight residual 109.52 120.99 -11.47 1.55e+00 4.16e-01 5.48e+01 angle pdb=" N TYR B 513 " pdb=" CA TYR B 513 " pdb=" C TYR B 513 " ideal model delta sigma weight residual 109.52 120.99 -11.47 1.55e+00 4.16e-01 5.48e+01 angle pdb=" N TYR A 513 " pdb=" CA TYR A 513 " pdb=" C TYR A 513 " ideal model delta sigma weight residual 109.52 120.98 -11.46 1.55e+00 4.16e-01 5.47e+01 angle pdb=" CB HIS C 136 " pdb=" CG HIS C 136 " pdb=" CD2 HIS C 136 " ideal model delta sigma weight residual 131.20 125.33 5.87 1.30e+00 5.92e-01 2.04e+01 ... (remaining 20575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 8504 21.76 - 43.53: 336 43.53 - 65.29: 68 65.29 - 87.05: 12 87.05 - 108.82: 4 Dihedral angle restraints: 8924 sinusoidal: 3220 harmonic: 5704 Sorted by residual: dihedral pdb=" CA TYR A 361 " pdb=" C TYR A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR B 361 " pdb=" C TYR B 361 " pdb=" N GLY B 362 " pdb=" CA GLY B 362 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR D 361 " pdb=" C TYR D 361 " pdb=" N GLY D 362 " pdb=" CA GLY D 362 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1418 0.074 - 0.148: 686 0.148 - 0.222: 132 0.222 - 0.296: 31 0.296 - 0.369: 9 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA ASP C 290 " pdb=" N ASP C 290 " pdb=" C ASP C 290 " pdb=" CB ASP C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA ASP B 290 " pdb=" N ASP B 290 " pdb=" C ASP B 290 " pdb=" CB ASP B 290 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA ASP D 290 " pdb=" N ASP D 290 " pdb=" C ASP D 290 " pdb=" CB ASP D 290 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 2273 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 281 " 0.185 2.00e-02 2.50e+03 8.99e-02 2.02e+02 pdb=" CG TRP B 281 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 281 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP B 281 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP B 281 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP B 281 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 281 " -0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 281 " 0.109 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 281 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP B 281 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 281 " -0.184 2.00e-02 2.50e+03 8.99e-02 2.02e+02 pdb=" CG TRP D 281 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 281 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP D 281 " 0.079 2.00e-02 2.50e+03 pdb=" NE1 TRP D 281 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP D 281 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 281 " 0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 281 " -0.109 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 281 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP D 281 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 281 " 0.184 2.00e-02 2.50e+03 8.98e-02 2.02e+02 pdb=" CG TRP C 281 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 281 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP C 281 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP C 281 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP C 281 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 281 " -0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 281 " 0.108 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 281 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 281 " 0.085 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 7488 3.03 - 3.50: 15740 3.50 - 3.96: 22934 3.96 - 4.43: 25800 4.43 - 4.90: 42992 Nonbonded interactions: 114954 Sorted by model distance: nonbonded pdb=" OH TYR B 435 " pdb=" OE2 GLU C 452 " model vdw 2.560 3.040 nonbonded pdb=" OH TYR A 435 " pdb=" OE2 GLU B 452 " model vdw 2.563 3.040 nonbonded pdb=" OH TYR D 435 " pdb=" OE2 GLU A 452 " model vdw 2.564 3.040 nonbonded pdb=" OG SER D 419 " pdb=" NZ LYS A 442 " model vdw 2.566 3.120 nonbonded pdb=" OG SER B 419 " pdb=" NZ LYS C 442 " model vdw 2.567 3.120 ... (remaining 114949 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.080 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: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.100 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.015 0.202 15192 Z= 0.945 Angle : 1.750 11.508 20580 Z= 1.175 Chirality : 0.087 0.369 2276 Planarity : 0.014 0.126 2604 Dihedral : 13.195 108.815 5236 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.22 % 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: -0.57 (0.19), residues: 1920 helix: -0.54 (0.13), residues: 1284 sheet: -1.61 (0.56), residues: 64 loop : 0.72 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.185 0.023 TRP B 281 HIS 0.009 0.003 HIS B 437 PHE 0.047 0.008 PHE B 186 TYR 0.115 0.016 TYR A 347 ARG 0.010 0.002 ARG C 428 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 1.492 Fit side-chains REVERT: D 101 MET cc_start: 0.7005 (mmt) cc_final: 0.6574 (mtt) REVERT: D 121 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6330 (mm-30) REVERT: D 189 ASP cc_start: 0.8439 (t70) cc_final: 0.8148 (t70) REVERT: D 287 MET cc_start: 0.6484 (mmm) cc_final: 0.5992 (mpp) REVERT: D 343 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7744 (mtmm) REVERT: D 408 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6909 (mp10) REVERT: D 412 LYS cc_start: 0.7397 (mttm) cc_final: 0.6842 (mttp) REVERT: D 429 GLN cc_start: 0.7356 (mm-40) cc_final: 0.6863 (mm110) REVERT: D 433 ASP cc_start: 0.7567 (t70) cc_final: 0.7042 (m-30) REVERT: D 451 ASN cc_start: 0.8147 (m-40) cc_final: 0.7828 (m110) REVERT: D 460 GLU cc_start: 0.8124 (tt0) cc_final: 0.7753 (tt0) REVERT: A 101 MET cc_start: 0.6956 (mmt) cc_final: 0.6510 (mtt) REVERT: A 121 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6307 (mm-30) REVERT: A 189 ASP cc_start: 0.8441 (t70) cc_final: 0.8115 (t70) REVERT: A 238 ILE cc_start: 0.7331 (tp) cc_final: 0.7126 (pp) REVERT: A 287 MET cc_start: 0.6397 (mmm) cc_final: 0.5950 (mpp) REVERT: A 343 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7780 (mtmm) REVERT: A 401 ASP cc_start: 0.6359 (p0) cc_final: 0.6133 (m-30) REVERT: A 408 GLN cc_start: 0.7324 (mm-40) cc_final: 0.6864 (mp10) REVERT: A 412 LYS cc_start: 0.7409 (mttm) cc_final: 0.6861 (mttp) REVERT: A 429 GLN cc_start: 0.7406 (mm-40) cc_final: 0.6836 (mm110) REVERT: A 433 ASP cc_start: 0.7515 (t70) cc_final: 0.6950 (m-30) REVERT: A 448 ASN cc_start: 0.7688 (t160) cc_final: 0.7419 (m110) REVERT: A 451 ASN cc_start: 0.8199 (m-40) cc_final: 0.7916 (m110) REVERT: A 460 GLU cc_start: 0.8128 (tt0) cc_final: 0.7848 (tt0) REVERT: B 101 MET cc_start: 0.7050 (mmt) cc_final: 0.6574 (mtt) REVERT: B 121 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6296 (mm-30) REVERT: B 189 ASP cc_start: 0.8407 (t70) cc_final: 0.8119 (t70) REVERT: B 238 ILE cc_start: 0.7336 (tp) cc_final: 0.7113 (pp) REVERT: B 287 MET cc_start: 0.6526 (mmm) cc_final: 0.6068 (mpp) REVERT: B 343 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7773 (mtmm) REVERT: B 408 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6919 (mp10) REVERT: B 412 LYS cc_start: 0.7414 (mttm) cc_final: 0.6898 (mttp) REVERT: B 429 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6923 (mm110) REVERT: B 433 ASP cc_start: 0.7511 (t70) cc_final: 0.6919 (m-30) REVERT: B 448 ASN cc_start: 0.7673 (t160) cc_final: 0.7386 (m110) REVERT: B 451 ASN cc_start: 0.8146 (m-40) cc_final: 0.7819 (m-40) REVERT: B 460 GLU cc_start: 0.8066 (tt0) cc_final: 0.7767 (tt0) REVERT: C 101 MET cc_start: 0.6985 (mmt) cc_final: 0.6549 (mtt) REVERT: C 121 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6266 (mm-30) REVERT: C 189 ASP cc_start: 0.8433 (t70) cc_final: 0.8208 (t70) REVERT: C 287 MET cc_start: 0.6515 (mmm) cc_final: 0.6017 (mpp) REVERT: C 343 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7764 (mtmm) REVERT: C 408 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6935 (mp10) REVERT: C 412 LYS cc_start: 0.7471 (mttm) cc_final: 0.6934 (mttp) REVERT: C 429 GLN cc_start: 0.7373 (mm-40) cc_final: 0.6872 (mm110) REVERT: C 433 ASP cc_start: 0.7589 (t70) cc_final: 0.6990 (m-30) REVERT: C 451 ASN cc_start: 0.8174 (m-40) cc_final: 0.7864 (m110) REVERT: C 460 GLU cc_start: 0.8151 (tt0) cc_final: 0.7866 (tt0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 1.1993 time to fit residues: 490.3576 Evaluate side-chains 244 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.0770 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 GLN D 344 GLN A 344 GLN A 448 ASN B 344 GLN B 448 ASN C 344 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15192 Z= 0.210 Angle : 0.545 5.542 20580 Z= 0.297 Chirality : 0.043 0.133 2276 Planarity : 0.004 0.036 2604 Dihedral : 9.825 76.056 2292 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.64 % Allowed : 10.19 % Favored : 88.17 % 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: 1.32 (0.19), residues: 1920 helix: 1.09 (0.14), residues: 1312 sheet: 0.10 (0.48), residues: 112 loop : 0.84 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 281 HIS 0.006 0.001 HIS A 437 PHE 0.016 0.001 PHE B 514 TYR 0.014 0.002 TYR D 289 ARG 0.008 0.001 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 251 time to evaluate : 1.495 Fit side-chains REVERT: D 101 MET cc_start: 0.7095 (mmt) cc_final: 0.6625 (mtt) REVERT: D 191 ILE cc_start: 0.7665 (pp) cc_final: 0.7431 (mt) REVERT: D 238 ILE cc_start: 0.7093 (tp) cc_final: 0.6681 (tp) REVERT: D 260 THR cc_start: 0.7845 (m) cc_final: 0.7630 (t) REVERT: D 283 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6133 (mm-30) REVERT: D 401 ASP cc_start: 0.6576 (p0) cc_final: 0.6312 (t0) REVERT: D 429 GLN cc_start: 0.7461 (mm-40) cc_final: 0.6773 (mm-40) REVERT: D 433 ASP cc_start: 0.7056 (t70) cc_final: 0.6830 (m-30) REVERT: D 448 ASN cc_start: 0.8105 (m-40) cc_final: 0.7748 (m-40) REVERT: D 451 ASN cc_start: 0.8260 (m-40) cc_final: 0.7958 (m-40) REVERT: D 460 GLU cc_start: 0.7920 (tt0) cc_final: 0.7428 (pt0) REVERT: D 494 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: A 101 MET cc_start: 0.7098 (mmt) cc_final: 0.6638 (mtt) REVERT: A 283 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6203 (mm-30) REVERT: A 398 GLN cc_start: 0.8243 (mt0) cc_final: 0.8001 (mt0) REVERT: A 401 ASP cc_start: 0.6596 (p0) cc_final: 0.6342 (t0) REVERT: A 408 GLN cc_start: 0.7282 (mm-40) cc_final: 0.7032 (mm-40) REVERT: A 429 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6888 (mm110) REVERT: A 448 ASN cc_start: 0.7546 (t0) cc_final: 0.7299 (m110) REVERT: A 451 ASN cc_start: 0.8250 (m-40) cc_final: 0.7871 (m-40) REVERT: A 460 GLU cc_start: 0.7939 (tt0) cc_final: 0.7349 (pt0) REVERT: A 494 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: A 554 ARG cc_start: 0.8373 (ptm-80) cc_final: 0.8111 (ptm160) REVERT: B 101 MET cc_start: 0.7196 (mmt) cc_final: 0.6719 (mtt) REVERT: B 283 GLU cc_start: 0.6837 (mt-10) cc_final: 0.6207 (mm-30) REVERT: B 408 GLN cc_start: 0.7277 (mm-40) cc_final: 0.7046 (mm-40) REVERT: B 429 GLN cc_start: 0.7326 (mm-40) cc_final: 0.6696 (mm-40) REVERT: B 433 ASP cc_start: 0.7091 (t70) cc_final: 0.6849 (m-30) REVERT: B 448 ASN cc_start: 0.7547 (t0) cc_final: 0.7281 (m110) REVERT: B 451 ASN cc_start: 0.8208 (m-40) cc_final: 0.7838 (m-40) REVERT: B 460 GLU cc_start: 0.7920 (tt0) cc_final: 0.7290 (pt0) REVERT: B 494 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: C 101 MET cc_start: 0.7097 (mmt) cc_final: 0.6621 (mtt) REVERT: C 238 ILE cc_start: 0.7127 (tp) cc_final: 0.6698 (tp) REVERT: C 256 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7546 (mm) REVERT: C 283 GLU cc_start: 0.6815 (mt-10) cc_final: 0.6140 (mm-30) REVERT: C 408 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7106 (mm-40) REVERT: C 429 GLN cc_start: 0.7337 (mm-40) cc_final: 0.6706 (mm-40) REVERT: C 433 ASP cc_start: 0.7035 (t70) cc_final: 0.6792 (m-30) REVERT: C 448 ASN cc_start: 0.8132 (m-40) cc_final: 0.7764 (m-40) REVERT: C 451 ASN cc_start: 0.8307 (m-40) cc_final: 0.8029 (m-40) REVERT: C 460 GLU cc_start: 0.7921 (tt0) cc_final: 0.7316 (pt0) REVERT: C 494 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7904 (mt-10) outliers start: 22 outliers final: 4 residues processed: 264 average time/residue: 1.0745 time to fit residues: 315.2777 Evaluate side-chains 243 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 234 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 20.0000 chunk 54 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 0.9980 chunk 188 optimal weight: 40.0000 chunk 155 optimal weight: 5.9990 chunk 173 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 140 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 GLN B 398 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15192 Z= 0.242 Angle : 0.525 5.591 20580 Z= 0.281 Chirality : 0.043 0.150 2276 Planarity : 0.004 0.055 2604 Dihedral : 8.772 65.608 2292 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.12 % Allowed : 12.20 % Favored : 86.68 % 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: 1.71 (0.19), residues: 1920 helix: 1.41 (0.14), residues: 1316 sheet: 0.05 (0.57), residues: 88 loop : 0.88 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 281 HIS 0.005 0.002 HIS C 437 PHE 0.016 0.002 PHE C 186 TYR 0.017 0.002 TYR C 347 ARG 0.005 0.001 ARG D 504 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 247 time to evaluate : 1.737 Fit side-chains REVERT: D 101 MET cc_start: 0.7024 (mmt) cc_final: 0.6589 (mtt) REVERT: D 260 THR cc_start: 0.7916 (m) cc_final: 0.7631 (t) REVERT: D 283 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6217 (mm-30) REVERT: D 429 GLN cc_start: 0.7431 (mm-40) cc_final: 0.6934 (tp40) REVERT: D 433 ASP cc_start: 0.7235 (t70) cc_final: 0.6863 (m-30) REVERT: D 448 ASN cc_start: 0.8152 (m-40) cc_final: 0.7815 (m-40) REVERT: D 451 ASN cc_start: 0.8294 (m-40) cc_final: 0.7968 (m-40) REVERT: D 460 GLU cc_start: 0.7945 (tt0) cc_final: 0.7285 (pt0) REVERT: D 494 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: A 101 MET cc_start: 0.7070 (mmt) cc_final: 0.6608 (mtt) REVERT: A 283 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6228 (mm-30) REVERT: A 401 ASP cc_start: 0.6602 (p0) cc_final: 0.6317 (m-30) REVERT: A 408 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7015 (mm-40) REVERT: A 448 ASN cc_start: 0.7545 (t0) cc_final: 0.7295 (m110) REVERT: A 451 ASN cc_start: 0.8260 (m-40) cc_final: 0.7939 (m-40) REVERT: A 460 GLU cc_start: 0.7976 (tt0) cc_final: 0.7284 (pt0) REVERT: A 494 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7861 (mt-10) REVERT: A 554 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.8103 (ptm160) REVERT: B 101 MET cc_start: 0.7103 (mmt) cc_final: 0.6644 (mtt) REVERT: B 238 ILE cc_start: 0.7307 (tp) cc_final: 0.6875 (tp) REVERT: B 283 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6280 (mm-30) REVERT: B 408 GLN cc_start: 0.7351 (mm-40) cc_final: 0.7054 (mm-40) REVERT: B 429 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6948 (tp40) REVERT: B 433 ASP cc_start: 0.7208 (t70) cc_final: 0.6857 (m-30) REVERT: B 448 ASN cc_start: 0.7545 (t0) cc_final: 0.7280 (m110) REVERT: B 451 ASN cc_start: 0.8268 (m-40) cc_final: 0.7958 (m-40) REVERT: B 460 GLU cc_start: 0.7970 (tt0) cc_final: 0.7369 (tt0) REVERT: B 484 VAL cc_start: 0.7592 (t) cc_final: 0.7382 (t) REVERT: B 494 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7942 (mt-10) REVERT: C 101 MET cc_start: 0.7015 (mmt) cc_final: 0.6567 (mtt) REVERT: C 238 ILE cc_start: 0.7282 (tp) cc_final: 0.6886 (tp) REVERT: C 283 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6249 (mm-30) REVERT: C 408 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7058 (mm-40) REVERT: C 429 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6913 (tp40) REVERT: C 448 ASN cc_start: 0.8154 (m-40) cc_final: 0.7837 (m-40) REVERT: C 451 ASN cc_start: 0.8266 (m-40) cc_final: 0.7942 (m-40) REVERT: C 460 GLU cc_start: 0.7957 (tt0) cc_final: 0.7220 (pt0) REVERT: C 494 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: C 554 ARG cc_start: 0.8465 (ttt-90) cc_final: 0.8250 (ttt-90) outliers start: 15 outliers final: 6 residues processed: 256 average time/residue: 1.1943 time to fit residues: 338.2295 Evaluate side-chains 224 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 214 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 chunk 90 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15192 Z= 0.166 Angle : 0.457 5.046 20580 Z= 0.245 Chirality : 0.040 0.146 2276 Planarity : 0.004 0.036 2604 Dihedral : 8.030 57.472 2292 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.82 % Allowed : 14.81 % Favored : 84.38 % 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: 2.04 (0.20), residues: 1920 helix: 1.66 (0.15), residues: 1320 sheet: 0.08 (0.57), residues: 88 loop : 1.04 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 281 HIS 0.004 0.001 HIS C 437 PHE 0.011 0.001 PHE B 186 TYR 0.015 0.001 TYR B 411 ARG 0.009 0.001 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 226 time to evaluate : 1.689 Fit side-chains REVERT: D 101 MET cc_start: 0.7036 (mmt) cc_final: 0.6616 (mtt) REVERT: D 191 ILE cc_start: 0.7861 (pp) cc_final: 0.7588 (mt) REVERT: D 260 THR cc_start: 0.7892 (m) cc_final: 0.7605 (t) REVERT: D 283 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6188 (mm-30) REVERT: D 429 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6934 (tp40) REVERT: D 433 ASP cc_start: 0.7180 (t70) cc_final: 0.6835 (m-30) REVERT: D 448 ASN cc_start: 0.8096 (m-40) cc_final: 0.7773 (m-40) REVERT: D 451 ASN cc_start: 0.8257 (m-40) cc_final: 0.7920 (m-40) REVERT: D 460 GLU cc_start: 0.7929 (tt0) cc_final: 0.7280 (pt0) REVERT: D 494 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: A 101 MET cc_start: 0.7059 (mmt) cc_final: 0.6613 (mtt) REVERT: A 283 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6187 (mm-30) REVERT: A 401 ASP cc_start: 0.6468 (p0) cc_final: 0.6177 (m-30) REVERT: A 408 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7101 (mm-40) REVERT: A 448 ASN cc_start: 0.7504 (t0) cc_final: 0.7254 (m110) REVERT: A 451 ASN cc_start: 0.8264 (m-40) cc_final: 0.7949 (m-40) REVERT: A 460 GLU cc_start: 0.7938 (tt0) cc_final: 0.7250 (pt0) REVERT: B 101 MET cc_start: 0.7037 (mmt) cc_final: 0.6594 (mtt) REVERT: B 283 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6206 (mm-30) REVERT: B 408 GLN cc_start: 0.7310 (mm-40) cc_final: 0.7031 (mm-40) REVERT: B 429 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7018 (tp40) REVERT: B 433 ASP cc_start: 0.7302 (t70) cc_final: 0.6924 (m-30) REVERT: B 448 ASN cc_start: 0.7442 (t0) cc_final: 0.7202 (m110) REVERT: B 451 ASN cc_start: 0.8284 (m-40) cc_final: 0.8003 (m-40) REVERT: B 460 GLU cc_start: 0.7958 (tt0) cc_final: 0.7252 (pt0) REVERT: B 484 VAL cc_start: 0.7544 (t) cc_final: 0.7328 (t) REVERT: B 487 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7326 (ttm) REVERT: B 494 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7946 (mt-10) REVERT: C 101 MET cc_start: 0.6994 (mmt) cc_final: 0.6567 (mtt) REVERT: C 238 ILE cc_start: 0.7275 (tp) cc_final: 0.6875 (tp) REVERT: C 283 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6182 (mm-30) REVERT: C 401 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: C 408 GLN cc_start: 0.7365 (mm-40) cc_final: 0.7049 (mm-40) REVERT: C 448 ASN cc_start: 0.8079 (m-40) cc_final: 0.7751 (m-40) REVERT: C 451 ASN cc_start: 0.8263 (m-40) cc_final: 0.7941 (m-40) REVERT: C 460 GLU cc_start: 0.7971 (tt0) cc_final: 0.7262 (pt0) REVERT: C 494 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: C 554 ARG cc_start: 0.8452 (ttt-90) cc_final: 0.8233 (ttt-90) outliers start: 11 outliers final: 1 residues processed: 232 average time/residue: 1.1591 time to fit residues: 297.8802 Evaluate side-chains 216 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 401 ASP Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 7.9990 chunk 105 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN B 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15192 Z= 0.265 Angle : 0.513 5.337 20580 Z= 0.271 Chirality : 0.042 0.148 2276 Planarity : 0.004 0.045 2604 Dihedral : 8.221 58.839 2292 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.56 % Allowed : 14.96 % Favored : 83.48 % 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: 1.87 (0.20), residues: 1920 helix: 1.57 (0.15), residues: 1324 sheet: 0.11 (0.58), residues: 88 loop : 0.83 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 281 HIS 0.004 0.001 HIS A 437 PHE 0.021 0.002 PHE A 186 TYR 0.018 0.002 TYR B 411 ARG 0.008 0.001 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 218 time to evaluate : 1.642 Fit side-chains REVERT: D 101 MET cc_start: 0.6943 (mmt) cc_final: 0.6542 (mtt) REVERT: D 283 GLU cc_start: 0.6884 (mt-10) cc_final: 0.6246 (mm-30) REVERT: D 401 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: D 429 GLN cc_start: 0.7426 (mm-40) cc_final: 0.6945 (tp40) REVERT: D 433 ASP cc_start: 0.7348 (t70) cc_final: 0.7113 (m-30) REVERT: D 448 ASN cc_start: 0.8097 (m-40) cc_final: 0.7731 (m-40) REVERT: D 460 GLU cc_start: 0.8023 (tt0) cc_final: 0.7189 (pt0) REVERT: D 494 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: A 101 MET cc_start: 0.6973 (mmt) cc_final: 0.6554 (mtt) REVERT: A 283 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6231 (mm-30) REVERT: A 448 ASN cc_start: 0.7464 (t0) cc_final: 0.7231 (m110) REVERT: A 451 ASN cc_start: 0.8279 (m-40) cc_final: 0.7960 (m110) REVERT: A 494 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: B 101 MET cc_start: 0.6943 (mmt) cc_final: 0.6530 (mtt) REVERT: B 283 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6254 (mm-30) REVERT: B 429 GLN cc_start: 0.7428 (mm-40) cc_final: 0.6982 (tp40) REVERT: B 433 ASP cc_start: 0.7398 (t70) cc_final: 0.7157 (m-30) REVERT: B 448 ASN cc_start: 0.7454 (t0) cc_final: 0.7215 (m110) REVERT: B 451 ASN cc_start: 0.8280 (m-40) cc_final: 0.7968 (m110) REVERT: B 484 VAL cc_start: 0.7607 (t) cc_final: 0.7388 (t) REVERT: B 487 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7497 (ttm) REVERT: B 494 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: C 101 MET cc_start: 0.6957 (mmt) cc_final: 0.6551 (mtt) REVERT: C 238 ILE cc_start: 0.7317 (tp) cc_final: 0.6909 (tp) REVERT: C 283 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6246 (mm-30) REVERT: C 448 ASN cc_start: 0.8102 (m-40) cc_final: 0.7755 (m-40) REVERT: C 487 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.7411 (ttm) REVERT: C 494 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8001 (mt-10) outliers start: 21 outliers final: 8 residues processed: 230 average time/residue: 1.2043 time to fit residues: 306.3906 Evaluate side-chains 221 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 401 ASP Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 459 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 185 optimal weight: 0.2980 chunk 154 optimal weight: 7.9990 chunk 86 optimal weight: 0.0670 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 overall best weight: 1.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 408 GLN B 408 GLN C 408 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15192 Z= 0.222 Angle : 0.482 5.487 20580 Z= 0.256 Chirality : 0.041 0.143 2276 Planarity : 0.004 0.035 2604 Dihedral : 8.080 58.362 2292 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.41 % Allowed : 15.33 % Favored : 83.26 % 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: 1.94 (0.20), residues: 1920 helix: 1.64 (0.15), residues: 1324 sheet: 0.17 (0.58), residues: 88 loop : 0.77 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 281 HIS 0.004 0.001 HIS A 437 PHE 0.014 0.001 PHE D 186 TYR 0.017 0.002 TYR B 411 ARG 0.008 0.001 ARG A 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 1.688 Fit side-chains REVERT: D 101 MET cc_start: 0.6943 (mmt) cc_final: 0.6547 (mtt) REVERT: D 283 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6210 (mm-30) REVERT: D 429 GLN cc_start: 0.7403 (mm-40) cc_final: 0.6927 (tp40) REVERT: D 433 ASP cc_start: 0.7279 (t70) cc_final: 0.6820 (m-30) REVERT: D 448 ASN cc_start: 0.8086 (m-40) cc_final: 0.7740 (m-40) REVERT: D 451 ASN cc_start: 0.8283 (m-40) cc_final: 0.7977 (m-40) REVERT: D 494 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: A 101 MET cc_start: 0.6960 (mmt) cc_final: 0.6552 (mtt) REVERT: A 283 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6214 (mm-30) REVERT: A 448 ASN cc_start: 0.7450 (t0) cc_final: 0.7222 (m110) REVERT: A 451 ASN cc_start: 0.8277 (m-40) cc_final: 0.7992 (m-40) REVERT: A 494 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: B 101 MET cc_start: 0.6966 (mmt) cc_final: 0.6549 (mtt) REVERT: B 283 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6226 (mm-30) REVERT: B 429 GLN cc_start: 0.7378 (mm-40) cc_final: 0.6894 (tp40) REVERT: B 433 ASP cc_start: 0.7306 (t70) cc_final: 0.6829 (m-30) REVERT: B 448 ASN cc_start: 0.7461 (t0) cc_final: 0.7220 (m110) REVERT: B 451 ASN cc_start: 0.8273 (m-40) cc_final: 0.7986 (m-40) REVERT: B 484 VAL cc_start: 0.7592 (t) cc_final: 0.7364 (t) REVERT: B 487 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7607 (ttm) REVERT: B 494 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: C 101 MET cc_start: 0.6930 (mmt) cc_final: 0.6530 (mtt) REVERT: C 238 ILE cc_start: 0.7419 (tp) cc_final: 0.6991 (tp) REVERT: C 283 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6213 (mm-30) REVERT: C 448 ASN cc_start: 0.8084 (m-40) cc_final: 0.7750 (m-40) REVERT: C 451 ASN cc_start: 0.8287 (m-40) cc_final: 0.7974 (m-40) REVERT: C 487 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7487 (ttm) REVERT: C 494 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7973 (mt-10) outliers start: 19 outliers final: 5 residues processed: 230 average time/residue: 1.1691 time to fit residues: 298.9787 Evaluate side-chains 213 residues out of total 1748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 202 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 71.9079 > 50: distance: 49 - 73: 24.589 distance: 54 - 82: 19.076 distance: 60 - 91: 23.201 distance: 63 - 73: 24.189 distance: 64 - 99: 8.559 distance: 73 - 74: 15.967 distance: 74 - 75: 28.136 distance: 74 - 77: 15.486 distance: 75 - 76: 8.257 distance: 75 - 82: 8.807 distance: 76 - 110: 23.986 distance: 77 - 78: 24.235 distance: 78 - 79: 7.786 distance: 79 - 80: 22.119 distance: 79 - 81: 18.483 distance: 82 - 83: 6.317 distance: 83 - 84: 7.365 distance: 83 - 86: 21.011 distance: 84 - 85: 7.132 distance: 84 - 91: 18.270 distance: 85 - 120: 19.650 distance: 86 - 87: 5.091 distance: 87 - 88: 26.209 distance: 88 - 90: 14.610 distance: 91 - 92: 5.476 distance: 92 - 93: 15.047 distance: 92 - 95: 4.112 distance: 93 - 94: 20.516 distance: 93 - 99: 14.374 distance: 94 - 128: 35.643 distance: 95 - 96: 20.067 distance: 95 - 97: 32.223 distance: 96 - 98: 24.086 distance: 99 - 100: 12.278 distance: 100 - 101: 24.814 distance: 100 - 103: 13.726 distance: 101 - 102: 20.592 distance: 101 - 110: 20.892 distance: 102 - 135: 17.169 distance: 103 - 104: 18.732 distance: 104 - 105: 20.288 distance: 104 - 106: 25.648 distance: 105 - 107: 10.490 distance: 106 - 108: 18.090 distance: 107 - 109: 29.508 distance: 108 - 109: 23.460 distance: 110 - 111: 32.731 distance: 111 - 112: 14.140 distance: 111 - 114: 42.265 distance: 112 - 113: 47.511 distance: 112 - 120: 38.769 distance: 114 - 115: 19.593 distance: 115 - 116: 21.635 distance: 115 - 117: 12.354 distance: 116 - 118: 14.710 distance: 117 - 119: 17.982 distance: 118 - 119: 11.262 distance: 120 - 121: 29.777 distance: 121 - 122: 11.018 distance: 121 - 124: 38.132 distance: 122 - 123: 38.557 distance: 122 - 128: 38.524 distance: 124 - 125: 50.861 distance: 126 - 127: 27.506 distance: 128 - 129: 18.387 distance: 129 - 130: 27.598 distance: 129 - 132: 36.998 distance: 130 - 131: 13.142 distance: 130 - 135: 6.658 distance: 132 - 134: 22.274 distance: 135 - 136: 22.162 distance: 136 - 137: 12.763 distance: 136 - 139: 26.575 distance: 137 - 138: 8.561 distance: 137 - 147: 8.325 distance: 139 - 140: 10.176 distance: 140 - 141: 5.845 distance: 140 - 142: 10.457 distance: 141 - 143: 5.410 distance: 142 - 144: 9.421 distance: 143 - 145: 5.734 distance: 144 - 145: 8.077 distance: 145 - 146: 21.822 distance: 147 - 148: 6.340 distance: 148 - 149: 12.520 distance: 148 - 151: 12.960 distance: 149 - 150: 20.047 distance: 149 - 155: 29.034 distance: 151 - 152: 11.542 distance: 152 - 153: 12.370 distance: 152 - 154: 19.799 distance: 155 - 156: 23.634 distance: 156 - 157: 24.577 distance: 156 - 159: 8.042 distance: 157 - 158: 25.273 distance: 157 - 163: 30.558 distance: 159 - 160: 13.035 distance: 160 - 161: 9.698 distance: 160 - 162: 18.059