Starting phenix.real_space_refine on Tue Nov 19 13:04:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/11_2024/5li4_4052.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/11_2024/5li4_4052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/11_2024/5li4_4052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/11_2024/5li4_4052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/11_2024/5li4_4052.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/11_2024/5li4_4052.cif" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.774 sd= 3.115 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 42 5.16 5 C 12660 2.51 5 N 3402 2.21 5 O 3966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 20070 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3345 Classifications: {'peptide': 427} Link IDs: {'CIS': 7, 'PTRANS': 10, 'TRANS': 409} Chain breaks: 9 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.79, per 1000 atoms: 0.39 Number of scatterers: 20070 At special positions: 0 Unit cell: (287.24, 276.92, 79.12, 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 42 16.00 O 3966 8.00 N 3402 7.00 C 12660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.71 Conformation dependent library (CDL) restraints added in 2.4 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB SER A 340 " pdb=" CB SER B 340 " pdb=" CB SER C 340 " pdb=" CB SER D 340 " pdb=" CB SER E 340 " pdb=" CB SER F 340 " Number of C-beta restraints generated: 4716 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 42 sheets defined 31.1% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU A 62 " --> pdb=" O GLN A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 Proline residue: A 80 - end of helix Processing helix chain 'A' and resid 150 through 169 Processing helix chain 'A' and resid 278 through 285 Processing helix chain 'A' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 4.033A pdb=" N SER A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 446 through 452 Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'A' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE A 513 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY A 514 " --> pdb=" O GLU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE A 524 " --> pdb=" O THR A 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 63 removed outlier: 3.595A pdb=" N LEU B 62 " --> pdb=" O GLN B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 82 Proline residue: B 80 - end of helix Processing helix chain 'B' and resid 150 through 169 Processing helix chain 'B' and resid 278 through 285 Processing helix chain 'B' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU B 324 " --> pdb=" O TRP B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER B 350 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE B 351 " --> pdb=" O GLU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU B 375 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 382 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 420 Processing helix chain 'B' and resid 446 through 452 Processing helix chain 'B' and resid 493 through 507 Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE B 513 " --> pdb=" O LEU B 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 514 " --> pdb=" O GLU B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE B 524 " --> pdb=" O THR B 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 Proline residue: C 80 - end of helix Processing helix chain 'C' and resid 150 through 169 Processing helix chain 'C' and resid 278 through 285 Processing helix chain 'C' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU C 324 " --> pdb=" O TRP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER C 350 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE C 351 " --> pdb=" O GLU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 382 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 420 Processing helix chain 'C' and resid 446 through 452 Processing helix chain 'C' and resid 493 through 507 Processing helix chain 'C' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE C 513 " --> pdb=" O LEU C 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY C 514 " --> pdb=" O GLU C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE C 524 " --> pdb=" O THR C 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 527 " --> pdb=" O SER C 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU D 62 " --> pdb=" O GLN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 Proline residue: D 80 - end of helix Processing helix chain 'D' and resid 150 through 169 Processing helix chain 'D' and resid 278 through 285 Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.218A pdb=" N LEU D 324 " --> pdb=" O TRP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 removed outlier: 4.033A pdb=" N SER D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE D 351 " --> pdb=" O GLU D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU D 375 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA D 382 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 420 Processing helix chain 'D' and resid 446 through 452 Processing helix chain 'D' and resid 493 through 507 Processing helix chain 'D' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE D 513 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 514 " --> pdb=" O GLU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE D 524 " --> pdb=" O THR D 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP D 527 " --> pdb=" O SER D 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.595A pdb=" N LEU E 62 " --> pdb=" O GLN E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 82 Proline residue: E 80 - end of helix Processing helix chain 'E' and resid 150 through 169 Processing helix chain 'E' and resid 278 through 285 Processing helix chain 'E' and resid 320 through 327 removed outlier: 4.218A pdb=" N LEU E 324 " --> pdb=" O TRP E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER E 350 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU E 375 " --> pdb=" O ASN E 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA E 382 " --> pdb=" O PHE E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 420 Processing helix chain 'E' and resid 446 through 452 Processing helix chain 'E' and resid 493 through 507 Processing helix chain 'E' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE E 513 " --> pdb=" O LEU E 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 514 " --> pdb=" O GLU E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE E 524 " --> pdb=" O THR E 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP E 527 " --> pdb=" O SER E 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.596A pdb=" N LEU F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 Proline residue: F 80 - end of helix Processing helix chain 'F' and resid 150 through 169 Processing helix chain 'F' and resid 278 through 285 Processing helix chain 'F' and resid 320 through 327 removed outlier: 4.217A pdb=" N LEU F 324 " --> pdb=" O TRP F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 353 removed outlier: 4.032A pdb=" N SER F 350 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE F 351 " --> pdb=" O GLU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 382 removed outlier: 3.786A pdb=" N GLU F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA F 382 " --> pdb=" O PHE F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 420 Processing helix chain 'F' and resid 446 through 452 Processing helix chain 'F' and resid 493 through 507 Processing helix chain 'F' and resid 508 through 515 removed outlier: 3.740A pdb=" N ILE F 513 " --> pdb=" O LEU F 508 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY F 514 " --> pdb=" O GLU F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 540 removed outlier: 3.739A pdb=" N ILE F 524 " --> pdb=" O THR F 520 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP F 527 " --> pdb=" O SER F 523 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.488A pdb=" N PHE A 36 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY A 40 " --> pdb=" O ILE A 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE A 143 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 137 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 145 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 123 " --> pdb=" O THR A 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A 131 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE A 119 " --> pdb=" O SER A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY A 253 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 460 through 462 Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 565 Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE B 36 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY B 40 " --> pdb=" O ILE B 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE B 143 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 137 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU B 145 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU B 123 " --> pdb=" O THR B 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 131 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE B 119 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY B 253 " --> pdb=" O LYS B 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 460 through 462 Processing sheet with id=AB5, first strand: chain 'B' and resid 561 through 565 Processing sheet with id=AB6, first strand: chain 'C' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE C 36 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY C 40 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AB9, first strand: chain 'C' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE C 143 " --> pdb=" O ILE C 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 137 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU C 145 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU C 123 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 131 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE C 119 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY C 253 " --> pdb=" O LYS C 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 460 through 462 Processing sheet with id=AC3, first strand: chain 'C' and resid 561 through 565 Processing sheet with id=AC4, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE D 36 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY D 40 " --> pdb=" O ILE D 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AC7, first strand: chain 'D' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE D 143 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE D 137 " --> pdb=" O PHE D 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU D 145 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU D 123 " --> pdb=" O THR D 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 131 " --> pdb=" O ILE D 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE D 119 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY D 253 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 460 through 462 Processing sheet with id=AD1, first strand: chain 'D' and resid 561 through 565 Processing sheet with id=AD2, first strand: chain 'E' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE E 36 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY E 40 " --> pdb=" O ILE E 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'E' and resid 106 through 108 Processing sheet with id=AD5, first strand: chain 'E' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE E 143 " --> pdb=" O ILE E 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE E 137 " --> pdb=" O PHE E 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU E 145 " --> pdb=" O ARG E 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR E 127 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU E 123 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER E 131 " --> pdb=" O ILE E 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE E 119 " --> pdb=" O SER E 131 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY E 253 " --> pdb=" O LYS E 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 460 through 462 Processing sheet with id=AD8, first strand: chain 'E' and resid 561 through 565 Processing sheet with id=AD9, first strand: chain 'F' and resid 52 through 53 removed outlier: 6.489A pdb=" N PHE F 36 " --> pdb=" O LEU F 88 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 40 through 41 removed outlier: 7.116A pdb=" N GLY F 40 " --> pdb=" O ILE F 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'F' and resid 106 through 108 Processing sheet with id=AE3, first strand: chain 'F' and resid 143 through 147 removed outlier: 6.856A pdb=" N PHE F 143 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE F 137 " --> pdb=" O PHE F 143 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU F 145 " --> pdb=" O ARG F 135 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N THR F 127 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU F 123 " --> pdb=" O THR F 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 131 " --> pdb=" O ILE F 119 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ILE F 119 " --> pdb=" O SER F 131 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 246 through 253 removed outlier: 6.375A pdb=" N GLY F 253 " --> pdb=" O LYS F 257 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 460 through 462 Processing sheet with id=AE6, first strand: chain 'F' and resid 561 through 565 600 hydrogen bonds defined for protein. 1728 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: 5.93 Time building geometry restraints manager: 6.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.43: 11205 1.43 - 1.74: 9045 1.74 - 2.06: 78 2.06 - 2.37: 12 2.37 - 2.68: 6 Bond restraints: 20346 Sorted by residual: bond pdb=" C ARG E 355 " pdb=" N GLU E 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG B 355 " pdb=" N GLU B 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG C 355 " pdb=" N GLU C 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG F 355 " pdb=" N GLU F 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 bond pdb=" C ARG A 355 " pdb=" N GLU A 360 " ideal model delta sigma weight residual 1.331 2.676 -1.345 2.07e-02 2.33e+03 4.22e+03 ... (remaining 20341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.92: 27144 10.92 - 21.83: 186 21.83 - 32.75: 54 32.75 - 43.66: 6 43.66 - 54.58: 6 Bond angle restraints: 27396 Sorted by residual: angle pdb=" O ARG C 355 " pdb=" C ARG C 355 " pdb=" N GLU C 360 " ideal model delta sigma weight residual 121.63 67.05 54.58 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG F 355 " pdb=" C ARG F 355 " pdb=" N GLU F 360 " ideal model delta sigma weight residual 121.63 67.05 54.58 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG A 355 " pdb=" C ARG A 355 " pdb=" N GLU A 360 " ideal model delta sigma weight residual 121.63 67.08 54.55 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG D 355 " pdb=" C ARG D 355 " pdb=" N GLU D 360 " ideal model delta sigma weight residual 121.63 67.08 54.55 1.52e+00 4.33e-01 1.29e+03 angle pdb=" O ARG E 355 " pdb=" C ARG E 355 " pdb=" N GLU E 360 " ideal model delta sigma weight residual 121.63 67.08 54.55 1.52e+00 4.33e-01 1.29e+03 ... (remaining 27391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.79: 11562 21.79 - 43.57: 444 43.57 - 65.36: 132 65.36 - 87.15: 48 87.15 - 108.93: 12 Dihedral angle restraints: 12198 sinusoidal: 4884 harmonic: 7314 Sorted by residual: dihedral pdb=" CA SER B 340 " pdb=" C SER B 340 " pdb=" N LYS B 341 " pdb=" CA LYS B 341 " ideal model delta harmonic sigma weight residual -180.00 -71.07 -108.93 0 5.00e+00 4.00e-02 4.75e+02 dihedral pdb=" CA SER E 340 " pdb=" C SER E 340 " pdb=" N LYS E 341 " pdb=" CA LYS E 341 " ideal model delta harmonic sigma weight residual -180.00 -71.07 -108.93 0 5.00e+00 4.00e-02 4.75e+02 dihedral pdb=" CA SER F 340 " pdb=" C SER F 340 " pdb=" N LYS F 341 " pdb=" CA LYS F 341 " ideal model delta harmonic sigma weight residual -180.00 -71.07 -108.93 0 5.00e+00 4.00e-02 4.75e+02 ... (remaining 12195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.989: 3078 0.989 - 1.978: 0 1.978 - 2.967: 0 2.967 - 3.956: 0 3.956 - 4.945: 6 Chirality restraints: 3084 Sorted by residual: chirality pdb=" CA SER C 340 " pdb=" N SER C 340 " pdb=" C SER C 340 " pdb=" CB SER C 340 " both_signs ideal model delta sigma weight residual False 2.51 -2.43 4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" CA SER F 340 " pdb=" N SER F 340 " pdb=" C SER F 340 " pdb=" CB SER F 340 " both_signs ideal model delta sigma weight residual False 2.51 -2.43 4.94 2.00e-01 2.50e+01 6.11e+02 chirality pdb=" CA SER A 340 " pdb=" N SER A 340 " pdb=" C SER A 340 " pdb=" CB SER A 340 " both_signs ideal model delta sigma weight residual False 2.51 -2.43 4.94 2.00e-01 2.50e+01 6.11e+02 ... (remaining 3081 not shown) Planarity restraints: 3570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 355 " -0.211 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C ARG E 355 " 0.474 2.00e-02 2.50e+03 pdb=" O ARG E 355 " -0.223 2.00e-02 2.50e+03 pdb=" N GLU E 360 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 355 " -0.211 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C ARG A 355 " 0.474 2.00e-02 2.50e+03 pdb=" O ARG A 355 " -0.223 2.00e-02 2.50e+03 pdb=" N GLU A 360 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 355 " -0.211 2.00e-02 2.50e+03 2.83e-01 8.02e+02 pdb=" C ARG D 355 " 0.474 2.00e-02 2.50e+03 pdb=" O ARG D 355 " -0.223 2.00e-02 2.50e+03 pdb=" N GLU D 360 " -0.040 2.00e-02 2.50e+03 ... (remaining 3567 not shown) Histogram of nonbonded interaction distances: 0.11 - 1.07: 66 1.07 - 2.03: 645 2.03 - 2.98: 15310 2.98 - 3.94: 55427 3.94 - 4.90: 100121 Warning: very small nonbonded interaction distances. Nonbonded interactions: 171569 Sorted by model distance: nonbonded pdb=" CD GLU C 93 " pdb=" CB ASP C 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU F 93 " pdb=" CB ASP F 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU B 93 " pdb=" CB ASP B 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU E 93 " pdb=" CB ASP E 140 " model vdw 0.111 3.670 nonbonded pdb=" CD GLU A 93 " pdb=" CB ASP A 140 " model vdw 0.112 3.670 ... (remaining 171564 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' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.230 Process input model: 40.080 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3172 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 : 0.053 1.345 20346 Z= 3.483 Angle : 3.066 54.579 27396 Z= 2.094 Chirality : 0.336 4.945 3084 Planarity : 0.019 0.283 3570 Dihedral : 14.438 108.931 7482 Min Nonbonded Distance : 0.111 Molprobity Statistics. All-atom Clashscore : 93.07 Ramachandran Plot: Outliers : 6.90 % Allowed : 14.04 % Favored : 79.06 % Rotamer: Outliers : 2.94 % Allowed : 4.50 % Favored : 92.56 % Cbeta Deviations : 4.82 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.47 % Twisted Proline : 11.11 % Twisted General : 2.21 % 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: -4.32 (0.14), residues: 2436 helix: -1.37 (0.21), residues: 612 sheet: -1.70 (0.27), residues: 246 loop : -3.99 (0.11), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.151 0.053 TRP D 320 HIS 0.009 0.002 HIS F 345 PHE 0.099 0.015 PHE C 351 TYR 0.236 0.016 TYR A 444 ARG 0.004 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 566 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ILE cc_start: 0.5185 (pt) cc_final: 0.4424 (pt) REVERT: A 50 VAL cc_start: 0.7572 (t) cc_final: 0.7067 (t) REVERT: B 39 ILE cc_start: 0.5546 (pt) cc_final: 0.5175 (pt) REVERT: B 153 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5838 (tp) REVERT: B 450 ASP cc_start: 0.6105 (p0) cc_final: 0.5884 (m-30) REVERT: C 39 ILE cc_start: 0.5845 (pt) cc_final: 0.5540 (pt) REVERT: C 576 VAL cc_start: 0.5496 (t) cc_final: 0.5293 (p) REVERT: D 39 ILE cc_start: 0.5158 (pt) cc_final: 0.4416 (pt) REVERT: D 50 VAL cc_start: 0.7567 (t) cc_final: 0.7068 (t) REVERT: E 39 ILE cc_start: 0.5540 (pt) cc_final: 0.5087 (pt) REVERT: E 153 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.5781 (tp) REVERT: E 450 ASP cc_start: 0.6113 (p0) cc_final: 0.5852 (m-30) REVERT: F 39 ILE cc_start: 0.5837 (pt) cc_final: 0.5539 (pt) REVERT: F 576 VAL cc_start: 0.5558 (t) cc_final: 0.5351 (p) outliers start: 64 outliers final: 26 residues processed: 624 average time/residue: 0.4193 time to fit residues: 369.0449 Evaluate side-chains 371 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 343 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 7.9990 chunk 191 optimal weight: 7.9990 chunk 105 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 58 GLN A 176 GLN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS A 530 GLN B 55 ASN B 176 GLN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN B 407 HIS B 530 GLN C 55 ASN C 58 GLN C 176 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 530 GLN D 55 ASN D 58 GLN D 176 GLN D 342 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 HIS D 530 GLN E 55 ASN E 58 GLN E 176 GLN ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN E 407 HIS E 530 GLN F 55 ASN F 58 GLN F 176 GLN ** F 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3320 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20346 Z= 0.395 Angle : 1.196 9.055 27396 Z= 0.642 Chirality : 0.067 0.379 3084 Planarity : 0.007 0.086 3570 Dihedral : 10.134 58.158 2730 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 32.88 Ramachandran Plot: Outliers : 1.39 % Allowed : 14.54 % Favored : 84.07 % Rotamer: Outliers : 0.87 % Allowed : 6.66 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 11.11 % Twisted General : 1.31 % 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: -4.38 (0.13), residues: 2448 helix: -1.31 (0.17), residues: 690 sheet: -1.72 (0.24), residues: 330 loop : -4.31 (0.11), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP B 76 HIS 0.006 0.002 HIS C 407 PHE 0.033 0.003 PHE D 143 TYR 0.026 0.003 TYR C 112 ARG 0.014 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 472 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 TRP cc_start: 0.5738 (t60) cc_final: 0.5130 (t60) REVERT: A 458 ILE cc_start: 0.3488 (mm) cc_final: 0.3229 (mm) REVERT: B 39 ILE cc_start: 0.5999 (pt) cc_final: 0.5692 (pt) REVERT: B 362 MET cc_start: 0.7100 (pmm) cc_final: 0.6760 (pmm) REVERT: C 53 LEU cc_start: 0.6801 (mt) cc_final: 0.6476 (mm) REVERT: C 62 LEU cc_start: 0.6430 (mt) cc_final: 0.6195 (mm) REVERT: C 326 LYS cc_start: 0.7877 (mttt) cc_final: 0.7230 (mttt) REVERT: D 76 TRP cc_start: 0.5773 (t60) cc_final: 0.5141 (t60) REVERT: D 458 ILE cc_start: 0.3536 (mm) cc_final: 0.3242 (mm) REVERT: E 39 ILE cc_start: 0.5954 (pt) cc_final: 0.5615 (pt) REVERT: E 362 MET cc_start: 0.7073 (pmm) cc_final: 0.6743 (pmm) REVERT: F 53 LEU cc_start: 0.6835 (mt) cc_final: 0.6514 (mm) REVERT: F 62 LEU cc_start: 0.6396 (mt) cc_final: 0.6137 (mm) REVERT: F 326 LYS cc_start: 0.7842 (mttt) cc_final: 0.7228 (mttt) outliers start: 19 outliers final: 0 residues processed: 490 average time/residue: 0.4031 time to fit residues: 281.7173 Evaluate side-chains 324 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 324 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 229 optimal weight: 30.0000 chunk 247 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: