Starting phenix.real_space_refine on Sat Sep 28 14:05:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/09_2024/5li4_4052.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/09_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_4052/09_2024/5li4_4052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/09_2024/5li4_4052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/09_2024/5li4_4052.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5li4_4052/09_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.92, 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: 5.88 Conformation dependent library (CDL) restraints added in 2.5 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: 2.26 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: 5.73 Time building geometry restraints manager: 6.70 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 40.390 Find NCS groups from input model: 0.850 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 64 poor density : 566 time to evaluate : 2.159 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: 0.3708 time to fit residues: 327.4329 Evaluate side-chains 371 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 343 time to evaluate : 2.262 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 19 poor density : 472 time to evaluate : 2.220 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: 0.3772 time to fit residues: 263.5609 Evaluate side-chains 324 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 2.312 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN B 120 GLN C 117 ASN C 407 HIS D 117 ASN D 497 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN E 120 GLN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN F 407 HIS F 530 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3424 moved from start: 0.8846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20346 Z= 0.304 Angle : 1.014 10.491 27396 Z= 0.540 Chirality : 0.058 0.460 3084 Planarity : 0.006 0.061 3570 Dihedral : 8.918 61.390 2730 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 27.37 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.97 % Favored : 84.80 % Rotamer: Outliers : 0.60 % Allowed : 5.33 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 11.11 % Twisted General : 0.82 % 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: -4.24 (0.13), residues: 2448 helix: -1.08 (0.18), residues: 690 sheet: -0.98 (0.27), residues: 294 loop : -4.40 (0.11), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP B 76 HIS 0.010 0.002 HIS F 407 PHE 0.032 0.002 PHE D 143 TYR 0.024 0.003 TYR B 112 ARG 0.012 0.001 ARG E 363 *********************** REFINEMENT MACRO_CYCLE 3 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 429 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 416 time to evaluate : 2.371 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: A 362 MET cc_start: 0.6431 (pmm) cc_final: 0.5472 (pmm) REVERT: B 362 MET cc_start: 0.7266 (pmm) cc_final: 0.6279 (pmm) REVERT: B 525 ILE cc_start: 0.5218 (mt) cc_final: 0.4965 (mt) REVERT: C 53 LEU cc_start: 0.6386 (mt) cc_final: 0.5855 (mm) REVERT: C 525 ILE cc_start: 0.5950 (mt) cc_final: 0.4870 (mt) REVERT: D 362 MET cc_start: 0.6460 (pmm) cc_final: 0.5523 (pmm) REVERT: E 362 MET cc_start: 0.7255 (pmm) cc_final: 0.6320 (pmm) REVERT: E 525 ILE cc_start: 0.5243 (mt) cc_final: 0.5009 (mt) REVERT: F 53 LEU cc_start: 0.6434 (mt) cc_final: 0.5853 (mm) REVERT: F 525 ILE cc_start: 0.5957 (mt) cc_final: 0.4858 (mt) outliers start: 13 outliers final: 6 residues processed: 428 average time/residue: 0.3988 time to fit residues: 240.1160 Evaluate side-chains 319 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 313 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.4980 chunk 172 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 153 optimal weight: 30.0000 chunk 230 optimal weight: 30.0000 chunk 243 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 30.0000 chunk 65 optimal weight: 20.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN D 120 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3498 moved from start: 1.0063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 20346 Z= 0.272 Angle : 0.956 10.634 27396 Z= 0.506 Chirality : 0.059 0.570 3084 Planarity : 0.006 0.055 3570 Dihedral : 8.250 55.136 2730 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 1.31 % Allowed : 13.24 % Favored : 85.46 % Rotamer: Outliers : 0.05 % Allowed : 5.92 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.74 % 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: -4.12 (0.14), residues: 2448 helix: -0.88 (0.19), residues: 684 sheet: -1.73 (0.28), residues: 282 loop : -4.14 (0.11), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP B 76 HIS 0.003 0.001 HIS D 171 PHE 0.026 0.002 PHE A 143 TYR 0.032 0.002 TYR C 566 ARG 0.007 0.001 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 4 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 424 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 2.335 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: A 362 MET cc_start: 0.6293 (pmm) cc_final: 0.5522 (pmm) REVERT: A 504 LEU cc_start: 0.5978 (mt) cc_final: 0.5699 (mt) REVERT: B 53 LEU cc_start: 0.6494 (mm) cc_final: 0.6230 (mm) REVERT: B 362 MET cc_start: 0.7267 (pmm) cc_final: 0.6861 (pmm) REVERT: B 525 ILE cc_start: 0.5720 (mt) cc_final: 0.4971 (mm) REVERT: C 76 TRP cc_start: 0.5121 (t60) cc_final: 0.4866 (t60) REVERT: C 343 SER cc_start: 0.7210 (m) cc_final: 0.6806 (p) REVERT: D 362 MET cc_start: 0.6295 (pmm) cc_final: 0.5575 (pmm) REVERT: D 504 LEU cc_start: 0.5944 (mt) cc_final: 0.5672 (mt) REVERT: E 53 LEU cc_start: 0.6275 (mm) cc_final: 0.5886 (mm) REVERT: E 362 MET cc_start: 0.7300 (pmm) cc_final: 0.6876 (pmm) REVERT: E 525 ILE cc_start: 0.5719 (mt) cc_final: 0.4994 (mm) REVERT: F 76 TRP cc_start: 0.5152 (t60) cc_final: 0.4890 (t60) REVERT: F 343 SER cc_start: 0.7235 (m) cc_final: 0.6845 (p) outliers start: 1 outliers final: 0 residues processed: 424 average time/residue: 0.3420 time to fit residues: 208.5248 Evaluate side-chains 332 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 207 optimal weight: 8.9990 chunk 168 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 218 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN C 342 GLN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN F 342 GLN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3413 moved from start: 1.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20346 Z= 0.237 Angle : 0.917 10.665 27396 Z= 0.485 Chirality : 0.056 0.512 3084 Planarity : 0.005 0.054 3570 Dihedral : 7.897 56.025 2730 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.66 % Favored : 86.44 % Rotamer: Outliers : 0.32 % Allowed : 4.59 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.69 % 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: -4.02 (0.14), residues: 2448 helix: -1.01 (0.18), residues: 696 sheet: -1.39 (0.27), residues: 294 loop : -4.07 (0.12), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 76 HIS 0.002 0.001 HIS D 345 PHE 0.035 0.002 PHE B 143 TYR 0.014 0.002 TYR E 532 ARG 0.007 0.001 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 5 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 427 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 420 time to evaluate : 2.283 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: A 52 GLU cc_start: 0.6221 (tm-30) cc_final: 0.5786 (tp30) REVERT: A 524 ILE cc_start: 0.3491 (mp) cc_final: 0.2987 (mp) REVERT: B 397 THR cc_start: -0.1632 (OUTLIER) cc_final: -0.2463 (p) REVERT: B 506 VAL cc_start: 0.6979 (p) cc_final: 0.6769 (p) REVERT: B 524 ILE cc_start: 0.4218 (mp) cc_final: 0.3353 (mp) REVERT: B 561 ILE cc_start: 0.4157 (tt) cc_final: 0.3909 (tt) REVERT: C 397 THR cc_start: -0.1071 (OUTLIER) cc_final: -0.1985 (p) REVERT: C 504 LEU cc_start: 0.4923 (mt) cc_final: 0.4518 (mt) REVERT: C 524 ILE cc_start: 0.2546 (mp) cc_final: 0.2280 (mp) REVERT: D 377 LEU cc_start: 0.6921 (mm) cc_final: 0.6672 (mm) REVERT: D 524 ILE cc_start: 0.3518 (mp) cc_final: 0.2997 (mp) REVERT: E 397 THR cc_start: -0.1634 (OUTLIER) cc_final: -0.2437 (p) REVERT: E 506 VAL cc_start: 0.6993 (p) cc_final: 0.6785 (p) REVERT: E 524 ILE cc_start: 0.4222 (mp) cc_final: 0.3430 (mp) REVERT: F 362 MET cc_start: 0.5783 (pmm) cc_final: 0.5510 (pmm) REVERT: F 397 THR cc_start: -0.1066 (OUTLIER) cc_final: -0.1982 (p) REVERT: F 504 LEU cc_start: 0.4902 (mt) cc_final: 0.4506 (mt) REVERT: F 524 ILE cc_start: 0.2590 (mp) cc_final: 0.2311 (mp) outliers start: 7 outliers final: 1 residues processed: 424 average time/residue: 0.3830 time to fit residues: 232.8093 Evaluate side-chains 322 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 317 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 243 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3522 moved from start: 1.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20346 Z= 0.256 Angle : 0.931 11.478 27396 Z= 0.494 Chirality : 0.055 0.461 3084 Planarity : 0.005 0.051 3570 Dihedral : 7.776 54.273 2730 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 1.14 % Allowed : 13.81 % Favored : 85.05 % Rotamer: Outliers : 0.09 % Allowed : 3.99 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -3.97 (0.14), residues: 2448 helix: -0.87 (0.18), residues: 690 sheet: -1.86 (0.27), residues: 306 loop : -3.97 (0.13), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP E 76 HIS 0.003 0.001 HIS D 171 PHE 0.032 0.002 PHE B 143 TYR 0.026 0.002 TYR A 566 ARG 0.016 0.001 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 6 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 392 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 390 time to evaluate : 2.284 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: A 362 MET cc_start: 0.5981 (pmm) cc_final: 0.5563 (pmm) REVERT: A 524 ILE cc_start: 0.4304 (mp) cc_final: 0.3419 (mp) REVERT: B 524 ILE cc_start: 0.4180 (mp) cc_final: 0.2823 (mp) REVERT: B 525 ILE cc_start: 0.6416 (mt) cc_final: 0.6169 (mm) REVERT: C 524 ILE cc_start: 0.2997 (mp) cc_final: 0.2275 (mp) REVERT: D 362 MET cc_start: 0.4956 (pmm) cc_final: 0.4726 (pmm) REVERT: D 524 ILE cc_start: 0.4327 (mp) cc_final: 0.3426 (mp) REVERT: E 52 GLU cc_start: 0.4378 (tm-30) cc_final: 0.3987 (tm-30) REVERT: E 524 ILE cc_start: 0.4206 (mp) cc_final: 0.2886 (mp) REVERT: E 525 ILE cc_start: 0.6444 (mt) cc_final: 0.6150 (mm) REVERT: F 524 ILE cc_start: 0.3037 (mp) cc_final: 0.2258 (mp) REVERT: F 529 ILE cc_start: 0.5922 (pt) cc_final: 0.5575 (pt) outliers start: 2 outliers final: 0 residues processed: 392 average time/residue: 0.3641 time to fit residues: 205.8845 Evaluate side-chains 315 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 30.0000 chunk 27 optimal weight: 30.0000 chunk 138 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 137 optimal weight: 0.0970 chunk 205 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 242 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3390 moved from start: 1.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20346 Z= 0.210 Angle : 0.865 9.744 27396 Z= 0.457 Chirality : 0.051 0.288 3084 Planarity : 0.005 0.056 3570 Dihedral : 7.393 55.050 2730 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.66 % Favored : 86.44 % Rotamer: Outliers : 0.05 % Allowed : 2.34 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -3.84 (0.15), residues: 2448 helix: -0.86 (0.18), residues: 684 sheet: -1.91 (0.27), residues: 306 loop : -3.78 (0.13), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP B 76 HIS 0.005 0.001 HIS F 407 PHE 0.037 0.001 PHE E 143 TYR 0.023 0.002 TYR C 411 ARG 0.009 0.001 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 7 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 393 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 392 time to evaluate : 2.229 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: A 362 MET cc_start: 0.5446 (pmm) cc_final: 0.4947 (pmm) REVERT: A 504 LEU cc_start: 0.5898 (mt) cc_final: 0.5379 (mt) REVERT: A 524 ILE cc_start: 0.3703 (mp) cc_final: 0.2528 (mp) REVERT: B 52 GLU cc_start: 0.5554 (tm-30) cc_final: 0.4121 (tm-30) REVERT: B 326 LYS cc_start: 0.7524 (pttt) cc_final: 0.7254 (pttt) REVERT: B 400 MET cc_start: 0.7304 (tmm) cc_final: 0.6430 (tmm) REVERT: B 524 ILE cc_start: 0.3377 (mp) cc_final: 0.1708 (mp) REVERT: B 525 ILE cc_start: 0.6484 (mt) cc_final: 0.6272 (mm) REVERT: C 53 LEU cc_start: 0.6087 (mm) cc_final: 0.5609 (mm) REVERT: C 400 MET cc_start: 0.7070 (tmm) cc_final: 0.6189 (tmm) REVERT: C 448 ASP cc_start: 0.4950 (t0) cc_final: 0.4706 (t0) REVERT: C 524 ILE cc_start: 0.2671 (mp) cc_final: 0.1709 (mp) REVERT: D 504 LEU cc_start: 0.5682 (mt) cc_final: 0.5393 (mt) REVERT: D 524 ILE cc_start: 0.3739 (mp) cc_final: 0.2533 (mp) REVERT: E 326 LYS cc_start: 0.7506 (ptpt) cc_final: 0.7274 (pttt) REVERT: E 400 MET cc_start: 0.7247 (tmm) cc_final: 0.6336 (tmm) REVERT: E 524 ILE cc_start: 0.3416 (mp) cc_final: 0.1782 (mp) REVERT: E 525 ILE cc_start: 0.6560 (mt) cc_final: 0.6282 (mm) REVERT: F 53 LEU cc_start: 0.6129 (mm) cc_final: 0.5613 (mm) REVERT: F 400 MET cc_start: 0.7049 (tmm) cc_final: 0.6134 (tmm) REVERT: F 524 ILE cc_start: 0.2723 (mp) cc_final: 0.1656 (mp) outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.3710 time to fit residues: 209.1290 Evaluate side-chains 303 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 30.0000 chunk 154 optimal weight: 7.9990 chunk 165 optimal weight: 20.0000 chunk 120 optimal weight: 0.0870 chunk 22 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 30.0000 overall best weight: 3.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 453 ASN ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 117 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 453 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 117 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3450 moved from start: 1.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20346 Z= 0.225 Angle : 0.866 9.714 27396 Z= 0.459 Chirality : 0.052 0.259 3084 Planarity : 0.005 0.060 3570 Dihedral : 7.389 52.735 2730 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.98 % Allowed : 13.52 % Favored : 85.50 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -3.81 (0.15), residues: 2448 helix: -0.78 (0.19), residues: 696 sheet: -1.76 (0.28), residues: 294 loop : -3.84 (0.13), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.004 TRP E 76 HIS 0.004 0.001 HIS B 345 PHE 0.043 0.002 PHE B 143 TYR 0.067 0.002 TYR A 56 ARG 0.011 0.001 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 8 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 385 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.282 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: A 462 PHE cc_start: 0.5479 (t80) cc_final: 0.5147 (t80) REVERT: A 524 ILE cc_start: 0.2355 (mp) cc_final: 0.1277 (mp) REVERT: B 52 GLU cc_start: 0.5694 (tm-30) cc_final: 0.4152 (tm-30) REVERT: B 62 LEU cc_start: 0.6592 (mm) cc_final: 0.6321 (mm) REVERT: B 400 MET cc_start: 0.7454 (tmm) cc_final: 0.6525 (tmm) REVERT: B 524 ILE cc_start: 0.3096 (mp) cc_final: 0.1612 (mp) REVERT: C 400 MET cc_start: 0.7211 (tmm) cc_final: 0.6392 (tmm) REVERT: C 524 ILE cc_start: 0.3272 (mp) cc_final: 0.2115 (mp) REVERT: D 524 ILE cc_start: 0.2429 (mp) cc_final: 0.1282 (mp) REVERT: E 326 LYS cc_start: 0.7231 (ptpt) cc_final: 0.6928 (pttt) REVERT: E 400 MET cc_start: 0.7396 (tmm) cc_final: 0.6469 (tmm) REVERT: E 524 ILE cc_start: 0.3133 (mp) cc_final: 0.1674 (mp) REVERT: F 400 MET cc_start: 0.7184 (tmm) cc_final: 0.6333 (tmm) REVERT: F 504 LEU cc_start: 0.5763 (mt) cc_final: 0.5552 (mt) REVERT: F 524 ILE cc_start: 0.3220 (mp) cc_final: 0.2071 (mp) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.3688 time to fit residues: 202.8857 Evaluate side-chains 300 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 2.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 177 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 214 optimal weight: 7.9990 chunk 225 optimal weight: 0.0370 chunk 148 optimal weight: 30.0000 overall best weight: 6.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN C 48 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 81 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN F 48 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 ASN ** F 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3684 moved from start: 1.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20346 Z= 0.290 Angle : 0.938 9.862 27396 Z= 0.494 Chirality : 0.054 0.316 3084 Planarity : 0.006 0.063 3570 Dihedral : 7.844 57.752 2730 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 27.32 Ramachandran Plot: Outliers : 1.14 % Allowed : 16.30 % Favored : 82.56 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -4.03 (0.14), residues: 2448 helix: -1.19 (0.17), residues: 714 sheet: -2.03 (0.27), residues: 306 loop : -3.84 (0.13), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.005 TRP B 76 HIS 0.004 0.002 HIS B 329 PHE 0.053 0.003 PHE D 143 TYR 0.042 0.003 TYR D 56 ARG 0.012 0.001 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 9 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 368 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 2.192 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: A 524 ILE cc_start: 0.3072 (mp) cc_final: 0.2399 (mp) REVERT: A 525 ILE cc_start: 0.6670 (mt) cc_final: 0.5841 (mm) REVERT: B 52 GLU cc_start: 0.5888 (tm-30) cc_final: 0.5130 (tm-30) REVERT: B 529 ILE cc_start: 0.6170 (pt) cc_final: 0.5447 (pt) REVERT: C 62 LEU cc_start: 0.6602 (mm) cc_final: 0.6369 (mm) REVERT: C 400 MET cc_start: 0.7117 (tmm) cc_final: 0.6308 (tmm) REVERT: C 504 LEU cc_start: 0.5286 (mt) cc_final: 0.4971 (mt) REVERT: C 524 ILE cc_start: 0.2015 (mp) cc_final: 0.0810 (mp) REVERT: C 525 ILE cc_start: 0.5972 (mt) cc_final: 0.5573 (mm) REVERT: D 52 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6350 (tp30) REVERT: D 62 LEU cc_start: 0.6597 (mm) cc_final: 0.6035 (mm) REVERT: D 524 ILE cc_start: 0.3074 (mp) cc_final: 0.2397 (mp) REVERT: D 525 ILE cc_start: 0.6874 (mt) cc_final: 0.6172 (mm) REVERT: E 529 ILE cc_start: 0.6196 (pt) cc_final: 0.5461 (pt) REVERT: F 56 TYR cc_start: 0.5124 (t80) cc_final: 0.4892 (t80) REVERT: F 62 LEU cc_start: 0.6589 (mm) cc_final: 0.6302 (mm) REVERT: F 400 MET cc_start: 0.7059 (tmm) cc_final: 0.6234 (tmm) REVERT: F 504 LEU cc_start: 0.5317 (mt) cc_final: 0.4940 (mt) REVERT: F 524 ILE cc_start: 0.1931 (mp) cc_final: 0.0815 (mp) REVERT: F 525 ILE cc_start: 0.6020 (mt) cc_final: 0.5612 (mm) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.3719 time to fit residues: 197.9313 Evaluate side-chains 301 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 30.0000 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 166 optimal weight: 40.0000 chunk 251 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 199 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 154 optimal weight: 2.9990 chunk 122 optimal weight: 0.3980 chunk 158 optimal weight: 20.0000 overall best weight: 6.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN ** E 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3748 moved from start: 1.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20346 Z= 0.289 Angle : 0.941 13.417 27396 Z= 0.499 Chirality : 0.053 0.270 3084 Planarity : 0.006 0.059 3570 Dihedral : 8.000 58.284 2730 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 1.18 % Allowed : 15.69 % Favored : 83.13 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -4.05 (0.14), residues: 2448 helix: -1.33 (0.17), residues: 708 sheet: -2.06 (0.28), residues: 306 loop : -3.77 (0.13), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP E 76 HIS 0.004 0.001 HIS C 407 PHE 0.048 0.003 PHE D 143 TYR 0.025 0.003 TYR C 411 ARG 0.014 0.001 ARG E 380 ********************** REFINEMENT MACRO_CYCLE 10 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 360 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.366 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: A 524 ILE cc_start: 0.2826 (mp) cc_final: 0.2260 (mp) REVERT: A 525 ILE cc_start: 0.6168 (mt) cc_final: 0.5396 (mm) REVERT: B 326 LYS cc_start: 0.6924 (pttt) cc_final: 0.6541 (pttt) REVERT: B 400 MET cc_start: 0.7929 (tmm) cc_final: 0.6941 (tmm) REVERT: C 54 ARG cc_start: 0.5808 (mtm-85) cc_final: 0.5600 (mtm-85) REVERT: C 326 LYS cc_start: 0.7427 (ptpt) cc_final: 0.7140 (ptpt) REVERT: C 400 MET cc_start: 0.7254 (tmm) cc_final: 0.6452 (tmm) REVERT: D 52 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6361 (tm-30) REVERT: D 62 LEU cc_start: 0.6573 (mm) cc_final: 0.5964 (mm) REVERT: F 62 LEU cc_start: 0.6423 (mm) cc_final: 0.6134 (mm) REVERT: F 326 LYS cc_start: 0.7441 (ptpt) cc_final: 0.7190 (ptpt) REVERT: F 400 MET cc_start: 0.7200 (tmm) cc_final: 0.6371 (tmm) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.3658 time to fit residues: 189.4734 Evaluate side-chains 311 residues out of total 2178 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 2.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 29 optimal weight: 40.0000 chunk 55 optimal weight: 7.9990 chunk 200 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 279 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.157142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.146100 restraints weight = 180988.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.146872 restraints weight = 148885.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.147750 restraints weight = 128434.075| |-----------------------------------------------------------------------------| r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 1.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20346 Z= 0.241 Angle : 0.908 13.061 27396 Z= 0.479 Chirality : 0.052 0.255 3084 Planarity : 0.006 0.087 3570 Dihedral : 7.784 58.141 2730 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 24.68 Ramachandran Plot: Outliers : 1.10 % Allowed : 15.24 % Favored : 83.66 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.61 % 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: -3.90 (0.15), residues: 2448 helix: -1.05 (0.18), residues: 714 sheet: -1.98 (0.29), residues: 306 loop : -3.78 (0.14), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP B 76 HIS 0.003 0.001 HIS D 171 PHE 0.039 0.002 PHE D 143 TYR 0.025 0.002 TYR E 532 ARG 0.014 0.001 ARG E 535 =============================================================================== Job complete usr+sys time: 4361.08 seconds wall clock time: 81 minutes 46.27 seconds (4906.27 seconds total)