Starting phenix.real_space_refine on Tue Jun 17 03:56:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5li4_4052/06_2025/5li4_4052.cif Found real_map, /net/cci-nas-00/data/ceres_data/5li4_4052/06_2025/5li4_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/cci-nas-00/data/ceres_data/5li4_4052/06_2025/5li4_4052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5li4_4052/06_2025/5li4_4052.map" model { file = "/net/cci-nas-00/data/ceres_data/5li4_4052/06_2025/5li4_4052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5li4_4052/06_2025/5li4_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.60, per 1000 atoms: 0.38 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: 5.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB SER A 340 " pdb=" CB SER B 340 " pdb=" CB SER C 340 " pdb=" CB SER D 340 " pdb=" CB SER E 340 " pdb=" CB SER F 340 " Number of C-beta restraints generated: 4716 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 42 sheets defined 31.1% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.35 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: 6.53 Time building geometry restraints manager: 6.27 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 40.730 Find NCS groups from input model: 0.410 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: 0.010 Load rotamer database and sin/cos tables:3.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.140 ------------------------------------------------------------------------------- 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= 3.441 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 Details of bonding type rmsd hydrogen bonds : bond 0.21354 ( 600) hydrogen bonds : angle 10.27849 ( 1728) covalent geometry : bond 0.05290 (20346) covalent geometry : angle 3.06564 (27396) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4872 Ramachandran restraints generated. 2436 Oldfield, 0 Emsley, 2436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 566 time to evaluate : 2.395 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: 0.4072 time to fit residues: 361.2217 Evaluate side-chains 371 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 343 time to evaluate : 2.269 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.168202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.156879 restraints weight = 181452.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.157903 restraints weight = 151022.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.158772 restraints weight = 128737.812| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 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= 0.286 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 Details of bonding type rmsd hydrogen bonds : bond 0.07393 ( 600) hydrogen bonds : angle 7.33879 ( 1728) covalent geometry : bond 0.00606 (20346) covalent geometry : angle 1.19598 (27396) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 472 time to evaluate : 2.219 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 60 LYS cc_start: 0.9547 (tttt) cc_final: 0.9333 (mtmm) REVERT: A 76 TRP cc_start: 0.7955 (t60) cc_final: 0.6813 (t60) REVERT: A 114 ASN cc_start: 0.9043 (t0) cc_final: 0.8629 (m-40) REVERT: A 138 PHE cc_start: 0.9331 (m-10) cc_final: 0.8944 (m-80) REVERT: A 504 LEU cc_start: 0.9016 (mt) cc_final: 0.8812 (mt) REVERT: A 524 ILE cc_start: 0.7863 (mt) cc_final: 0.7462 (mt) REVERT: B 49 THR cc_start: 0.7939 (m) cc_final: 0.7559 (p) REVERT: B 76 TRP cc_start: 0.7612 (t60) cc_final: 0.7020 (t60) REVERT: B 88 LEU cc_start: 0.9607 (mt) cc_final: 0.9304 (mt) REVERT: B 114 ASN cc_start: 0.8976 (t0) cc_final: 0.8678 (m-40) REVERT: B 138 PHE cc_start: 0.9102 (m-10) cc_final: 0.8843 (m-80) REVERT: B 362 MET cc_start: 0.7005 (pmm) cc_final: 0.6707 (pmm) REVERT: B 411 TYR cc_start: 0.4989 (m-80) cc_final: 0.4757 (m-10) REVERT: B 417 LEU cc_start: 0.9663 (mt) cc_final: 0.9431 (pp) REVERT: B 504 LEU cc_start: 0.8649 (mt) cc_final: 0.8388 (mt) REVERT: B 524 ILE cc_start: 0.8058 (mt) cc_final: 0.7771 (mt) REVERT: C 35 VAL cc_start: 0.9095 (m) cc_final: 0.8774 (p) REVERT: C 49 THR cc_start: 0.8697 (m) cc_final: 0.8220 (p) REVERT: C 51 TYR cc_start: 0.6822 (t80) cc_final: 0.6503 (t80) REVERT: C 53 LEU cc_start: 0.9217 (mt) cc_final: 0.8662 (mm) REVERT: C 114 ASN cc_start: 0.9207 (t0) cc_final: 0.8980 (m-40) REVERT: C 351 PHE cc_start: 0.8403 (m-80) cc_final: 0.8154 (m-80) REVERT: C 411 TYR cc_start: 0.6668 (m-80) cc_final: 0.6078 (m-10) REVERT: C 417 LEU cc_start: 0.9629 (mt) cc_final: 0.9349 (pp) REVERT: C 452 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6403 (pp) REVERT: C 504 LEU cc_start: 0.8828 (mt) cc_final: 0.8571 (mt) REVERT: C 505 LYS cc_start: 0.8497 (tptt) cc_final: 0.8254 (mttt) REVERT: C 524 ILE cc_start: 0.7631 (mt) cc_final: 0.7291 (mt) REVERT: C 557 ASN cc_start: 0.5888 (t0) cc_final: 0.5604 (p0) REVERT: D 76 TRP cc_start: 0.7959 (t60) cc_final: 0.6816 (t60) REVERT: D 114 ASN cc_start: 0.9066 (t0) cc_final: 0.8643 (m-40) REVERT: D 138 PHE cc_start: 0.9350 (m-10) cc_final: 0.8956 (m-80) REVERT: D 376 GLN cc_start: 0.8899 (pt0) cc_final: 0.8699 (pm20) REVERT: D 504 LEU cc_start: 0.9013 (mt) cc_final: 0.8808 (mt) REVERT: D 524 ILE cc_start: 0.7883 (mt) cc_final: 0.7491 (mt) REVERT: E 49 THR cc_start: 0.7991 (m) cc_final: 0.7593 (p) REVERT: E 76 TRP cc_start: 0.7577 (t60) cc_final: 0.6991 (t60) REVERT: E 88 LEU cc_start: 0.9604 (mt) cc_final: 0.9302 (mt) REVERT: E 114 ASN cc_start: 0.9007 (t0) cc_final: 0.8700 (m-40) REVERT: E 138 PHE cc_start: 0.9097 (m-10) cc_final: 0.8845 (m-80) REVERT: E 362 MET cc_start: 0.7031 (pmm) cc_final: 0.6732 (pmm) REVERT: E 411 TYR cc_start: 0.4920 (m-80) cc_final: 0.4703 (m-10) REVERT: E 417 LEU cc_start: 0.9668 (mt) cc_final: 0.9439 (pp) REVERT: E 504 LEU cc_start: 0.8631 (mt) cc_final: 0.8369 (mt) REVERT: E 524 ILE cc_start: 0.8054 (mt) cc_final: 0.7763 (mt) REVERT: F 35 VAL cc_start: 0.9097 (m) cc_final: 0.8783 (p) REVERT: F 49 THR cc_start: 0.8751 (m) cc_final: 0.8265 (p) REVERT: F 51 TYR cc_start: 0.6817 (t80) cc_final: 0.6493 (t80) REVERT: F 53 LEU cc_start: 0.9216 (mt) cc_final: 0.8649 (mm) REVERT: F 114 ASN cc_start: 0.9197 (t0) cc_final: 0.8974 (m-40) REVERT: F 351 PHE cc_start: 0.8407 (m-80) cc_final: 0.8162 (m-80) REVERT: F 411 TYR cc_start: 0.6648 (m-80) cc_final: 0.6059 (m-10) REVERT: F 417 LEU cc_start: 0.9639 (mt) cc_final: 0.9360 (pp) REVERT: F 452 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6353 (pp) REVERT: F 504 LEU cc_start: 0.8815 (mt) cc_final: 0.8559 (mt) REVERT: F 505 LYS cc_start: 0.8489 (tptt) cc_final: 0.8250 (mttt) REVERT: F 524 ILE cc_start: 0.7589 (mt) cc_final: 0.7257 (mt) REVERT: F 557 ASN cc_start: 0.5860 (t0) cc_final: 0.5591 (p0) outliers start: 19 outliers final: 0 residues processed: 490 average time/residue: 0.3808 time to fit residues: 267.4481 Evaluate side-chains 334 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 332 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 144 optimal weight: 30.0000 chunk 76 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 20.0000 chunk 179 optimal weight: 0.0980 chunk 132 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 530 GLN B 117 ASN C 117 ASN D 117 ASN D 530 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.167666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.155989 restraints weight = 181434.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.156973 restraints weight = 154926.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.157427 restraints weight = 135292.084| |-----------------------------------------------------------------------------| r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5583 moved from start: 0.8812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 20346 Z= 0.195 Angle : 0.968 10.669 27396 Z= 0.516 Chirality : 0.056 0.383 3084 Planarity : 0.005 0.062 3570 Dihedral : 8.570 61.841 2730 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 22.59 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.52 % Favored : 85.25 % Rotamer: Outliers : 0.18 % Allowed : 5.37 % Favored : 94.44 % 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: -4.08 (0.14), residues: 2448 helix: -0.92 (0.18), residues: 690 sheet: -0.83 (0.27), residues: 294 loop : -4.33 (0.11), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 76 HIS 0.006 0.002 HIS F 407 PHE 0.034 0.002 PHE D 143 TYR 0.020 0.002 TYR F 532 ARG 0.004 0.001 ARG B 538 Details of bonding type rmsd hydrogen bonds : bond 0.05725 ( 600) hydrogen bonds : angle 6.52588 ( 1728) covalent geometry : bond 0.00407 (20346) covalent geometry : angle 0.96796 (27396) *********************** 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 439 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 435 time to evaluate : 2.291 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: A 51 TYR cc_start: 0.6380 (t80) cc_final: 0.6030 (t80) REVERT: A 326 LYS cc_start: 0.9515 (mtpt) cc_final: 0.9312 (ptmt) REVERT: A 342 GLN cc_start: 0.8792 (pp30) cc_final: 0.8185 (mp10) REVERT: A 353 LYS cc_start: 0.9402 (pptt) cc_final: 0.9135 (mttp) REVERT: A 362 MET cc_start: 0.7587 (pmm) cc_final: 0.6618 (pmm) REVERT: A 381 GLN cc_start: 0.3920 (tt0) cc_final: 0.2913 (tt0) REVERT: A 524 ILE cc_start: 0.7979 (mt) cc_final: 0.7743 (mt) REVERT: B 60 LYS cc_start: 0.9445 (mttt) cc_final: 0.9238 (mmmt) REVERT: B 326 LYS cc_start: 0.9325 (mtmt) cc_final: 0.9097 (mtmt) REVERT: B 342 GLN cc_start: 0.9135 (pp30) cc_final: 0.8421 (mm110) REVERT: B 353 LYS cc_start: 0.9391 (pptt) cc_final: 0.8940 (mttp) REVERT: B 362 MET cc_start: 0.7859 (pmm) cc_final: 0.6952 (pmm) REVERT: B 448 ASP cc_start: 0.9445 (t0) cc_final: 0.8730 (p0) REVERT: B 524 ILE cc_start: 0.8210 (mt) cc_final: 0.7964 (mt) REVERT: C 51 TYR cc_start: 0.6284 (t80) cc_final: 0.5827 (t80) REVERT: C 53 LEU cc_start: 0.9253 (mt) cc_final: 0.8811 (mm) REVERT: C 56 TYR cc_start: 0.8603 (t80) cc_final: 0.7985 (t80) REVERT: C 326 LYS cc_start: 0.9159 (mttt) cc_final: 0.8947 (mttt) REVERT: C 362 MET cc_start: 0.6887 (pmm) cc_final: 0.6456 (pmm) REVERT: C 504 LEU cc_start: 0.8475 (mt) cc_final: 0.8179 (mt) REVERT: C 524 ILE cc_start: 0.7844 (mt) cc_final: 0.7476 (mt) REVERT: D 51 TYR cc_start: 0.6396 (t80) cc_final: 0.6077 (t80) REVERT: D 342 GLN cc_start: 0.8787 (pp30) cc_final: 0.8156 (mp10) REVERT: D 353 LYS cc_start: 0.9431 (pptt) cc_final: 0.9149 (mttp) REVERT: D 362 MET cc_start: 0.7581 (pmm) cc_final: 0.6634 (pmm) REVERT: D 461 GLU cc_start: 0.7537 (pp20) cc_final: 0.7322 (pp20) REVERT: D 524 ILE cc_start: 0.8030 (mt) cc_final: 0.7784 (mt) REVERT: E 326 LYS cc_start: 0.9324 (mtmt) cc_final: 0.9106 (mtmt) REVERT: E 342 GLN cc_start: 0.9143 (pp30) cc_final: 0.8412 (mm110) REVERT: E 353 LYS cc_start: 0.9372 (pptt) cc_final: 0.8936 (mttp) REVERT: E 362 MET cc_start: 0.7858 (pmm) cc_final: 0.6950 (pmm) REVERT: E 448 ASP cc_start: 0.9433 (t0) cc_final: 0.8718 (p0) REVERT: E 524 ILE cc_start: 0.8150 (mt) cc_final: 0.7915 (mt) REVERT: F 51 TYR cc_start: 0.6342 (t80) cc_final: 0.5856 (t80) REVERT: F 53 LEU cc_start: 0.9269 (mt) cc_final: 0.8823 (mm) REVERT: F 56 TYR cc_start: 0.8620 (t80) cc_final: 0.7975 (t80) REVERT: F 326 LYS cc_start: 0.9165 (mttt) cc_final: 0.8957 (mttt) REVERT: F 353 LYS cc_start: 0.9154 (pptt) cc_final: 0.8948 (ptpp) REVERT: F 362 MET cc_start: 0.6860 (pmm) cc_final: 0.6443 (pmm) REVERT: F 504 LEU cc_start: 0.8503 (mt) cc_final: 0.8205 (mt) REVERT: F 524 ILE cc_start: 0.7835 (mt) cc_final: 0.7464 (mt) outliers start: 4 outliers final: 4 residues processed: 439 average time/residue: 0.3967 time to fit residues: 246.1723 Evaluate side-chains 333 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 329 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 140 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 235 optimal weight: 0.0870 chunk 206 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 78 optimal weight: 0.0670 chunk 68 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 170 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 overall best weight: 4.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 342 GLN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN E 342 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 GLN F 530 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.165137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.153597 restraints weight = 178703.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.154499 restraints weight = 152771.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.154991 restraints weight = 133694.078| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.9743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 20346 Z= 0.193 Angle : 0.928 9.937 27396 Z= 0.493 Chirality : 0.056 0.500 3084 Planarity : 0.006 0.090 3570 Dihedral : 8.028 54.586 2730 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 1.14 % Allowed : 13.07 % Favored : 85.78 % Rotamer: Outliers : 0.28 % Allowed : 4.55 % Favored : 95.18 % 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: -3.93 (0.14), residues: 2448 helix: -0.54 (0.19), residues: 666 sheet: -1.28 (0.27), residues: 306 loop : -4.21 (0.11), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 320 HIS 0.006 0.001 HIS C 407 PHE 0.024 0.002 PHE B 143 TYR 0.035 0.002 TYR F 411 ARG 0.007 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.05387 ( 600) hydrogen bonds : angle 6.44766 ( 1728) covalent geometry : bond 0.00406 (20346) covalent geometry : angle 0.92830 (27396) *********************** 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 444 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 438 time to evaluate : 2.007 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: A 39 ILE cc_start: 0.9331 (pt) cc_final: 0.9128 (pt) REVERT: A 51 TYR cc_start: 0.6899 (t80) cc_final: 0.6336 (t80) REVERT: A 52 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8410 (tp30) REVERT: A 60 LYS cc_start: 0.9457 (tttt) cc_final: 0.9136 (tppt) REVERT: A 342 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: A 362 MET cc_start: 0.7151 (pmm) cc_final: 0.6551 (pmm) REVERT: A 411 TYR cc_start: 0.5895 (m-80) cc_final: 0.5186 (m-10) REVERT: A 461 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7982 (mp0) REVERT: A 504 LEU cc_start: 0.8987 (mt) cc_final: 0.8772 (mt) REVERT: A 524 ILE cc_start: 0.8435 (mt) cc_final: 0.8006 (mt) REVERT: B 51 TYR cc_start: 0.6833 (t80) cc_final: 0.6313 (t80) REVERT: B 52 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7655 (tm-30) REVERT: B 61 ARG cc_start: 0.9391 (ttp-110) cc_final: 0.9118 (ptp-110) REVERT: B 326 LYS cc_start: 0.9035 (mtmt) cc_final: 0.8790 (mtmt) REVERT: B 342 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.8375 (mm-40) REVERT: B 451 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8719 (pp20) REVERT: B 504 LEU cc_start: 0.8865 (mt) cc_final: 0.8664 (mt) REVERT: B 524 ILE cc_start: 0.8388 (mt) cc_final: 0.8171 (mt) REVERT: C 51 TYR cc_start: 0.6950 (t80) cc_final: 0.6663 (t80) REVERT: C 52 GLU cc_start: 0.8659 (pp20) cc_final: 0.8273 (pp20) REVERT: C 53 LEU cc_start: 0.9432 (mt) cc_final: 0.9118 (mt) REVERT: C 55 ASN cc_start: 0.9138 (m110) cc_final: 0.8817 (m-40) REVERT: C 76 TRP cc_start: 0.6709 (t60) cc_final: 0.6348 (t60) REVERT: C 326 LYS cc_start: 0.9306 (mttt) cc_final: 0.8986 (mttt) REVERT: C 351 PHE cc_start: 0.9008 (m-80) cc_final: 0.8608 (m-80) REVERT: C 362 MET cc_start: 0.7112 (pmm) cc_final: 0.6905 (pmm) REVERT: C 394 ASN cc_start: 0.7456 (m110) cc_final: 0.7232 (m110) REVERT: C 461 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8575 (mp0) REVERT: C 504 LEU cc_start: 0.8697 (mt) cc_final: 0.8382 (mt) REVERT: C 524 ILE cc_start: 0.8259 (mt) cc_final: 0.7905 (mt) REVERT: D 39 ILE cc_start: 0.9372 (pt) cc_final: 0.9130 (pt) REVERT: D 51 TYR cc_start: 0.6912 (t80) cc_final: 0.6282 (t80) REVERT: D 61 ARG cc_start: 0.9562 (ttp-110) cc_final: 0.9201 (ptp-110) REVERT: D 342 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.8157 (mm-40) REVERT: D 362 MET cc_start: 0.7223 (pmm) cc_final: 0.6814 (pmm) REVERT: D 411 TYR cc_start: 0.5931 (m-80) cc_final: 0.5353 (m-10) REVERT: D 461 GLU cc_start: 0.7673 (pp20) cc_final: 0.7203 (pp20) REVERT: D 504 LEU cc_start: 0.8978 (mt) cc_final: 0.8763 (mt) REVERT: D 524 ILE cc_start: 0.8443 (mt) cc_final: 0.8012 (mt) REVERT: E 51 TYR cc_start: 0.6800 (t80) cc_final: 0.6286 (t80) REVERT: E 52 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7539 (tm-30) REVERT: E 60 LYS cc_start: 0.9654 (mmtm) cc_final: 0.9244 (mmmt) REVERT: E 62 LEU cc_start: 0.9610 (mm) cc_final: 0.9402 (mm) REVERT: E 326 LYS cc_start: 0.9055 (mtmt) cc_final: 0.8811 (mtmt) REVERT: E 342 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.8399 (mm-40) REVERT: E 451 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8734 (pp20) REVERT: E 524 ILE cc_start: 0.8351 (mt) cc_final: 0.8148 (mt) REVERT: F 51 TYR cc_start: 0.6942 (t80) cc_final: 0.6652 (t80) REVERT: F 52 GLU cc_start: 0.8639 (pp20) cc_final: 0.8252 (pp20) REVERT: F 53 LEU cc_start: 0.9437 (mt) cc_final: 0.9105 (mt) REVERT: F 55 ASN cc_start: 0.9131 (m110) cc_final: 0.8808 (m-40) REVERT: F 76 TRP cc_start: 0.6668 (t60) cc_final: 0.6307 (t60) REVERT: F 326 LYS cc_start: 0.9323 (mttt) cc_final: 0.9005 (mttt) REVERT: F 351 PHE cc_start: 0.9047 (m-80) cc_final: 0.8649 (m-80) REVERT: F 353 LYS cc_start: 0.9497 (pptt) cc_final: 0.9109 (ptpp) REVERT: F 362 MET cc_start: 0.7133 (pmm) cc_final: 0.6911 (pmm) REVERT: F 394 ASN cc_start: 0.7359 (m110) cc_final: 0.7157 (m110) REVERT: F 461 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8574 (mp0) REVERT: F 504 LEU cc_start: 0.8685 (mt) cc_final: 0.8371 (mt) REVERT: F 524 ILE cc_start: 0.8248 (mt) cc_final: 0.7892 (mt) outliers start: 6 outliers final: 0 residues processed: 440 average time/residue: 0.3612 time to fit residues: 229.6283 Evaluate side-chains 354 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 350 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 195 optimal weight: 30.0000 chunk 127 optimal weight: 9.9990 chunk 89 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 172 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 110 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 58 optimal weight: 0.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 GLN E 342 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.165012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.153863 restraints weight = 180061.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.154864 restraints weight = 150776.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.155573 restraints weight = 129358.136| |-----------------------------------------------------------------------------| r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5777 moved from start: 1.0463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20346 Z= 0.185 Angle : 0.895 10.437 27396 Z= 0.475 Chirality : 0.055 0.483 3084 Planarity : 0.005 0.063 3570 Dihedral : 7.699 54.791 2730 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.28 % Favored : 85.78 % Rotamer: Outliers : 0.05 % Allowed : 4.55 % Favored : 95.41 % 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: -3.89 (0.14), residues: 2448 helix: -0.56 (0.19), residues: 672 sheet: -1.64 (0.26), residues: 300 loop : -4.06 (0.12), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 320 HIS 0.005 0.001 HIS A 345 PHE 0.032 0.002 PHE B 143 TYR 0.016 0.002 TYR D 411 ARG 0.008 0.001 ARG E 61 Details of bonding type rmsd hydrogen bonds : bond 0.05351 ( 600) hydrogen bonds : angle 6.30949 ( 1728) covalent geometry : bond 0.00383 (20346) covalent geometry : angle 0.89473 (27396) *********************** 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 429 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 428 time to evaluate : 2.231 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 41 GLN cc_start: 0.9197 (mp10) cc_final: 0.8954 (mp10) REVERT: A 51 TYR cc_start: 0.7037 (t80) cc_final: 0.6397 (t80) REVERT: A 60 LYS cc_start: 0.9480 (tttt) cc_final: 0.9261 (tppt) REVERT: A 326 LYS cc_start: 0.9377 (mtmt) cc_final: 0.9144 (ptpt) REVERT: A 342 GLN cc_start: 0.9103 (pp30) cc_final: 0.8141 (mp10) REVERT: A 524 ILE cc_start: 0.8795 (mt) cc_final: 0.8245 (mt) REVERT: B 51 TYR cc_start: 0.6953 (t80) cc_final: 0.6196 (t80) REVERT: B 53 LEU cc_start: 0.9143 (mm) cc_final: 0.8902 (mm) REVERT: B 56 TYR cc_start: 0.9004 (t80) cc_final: 0.8755 (t80) REVERT: B 342 GLN cc_start: 0.9450 (pp30) cc_final: 0.8344 (mm-40) REVERT: B 351 PHE cc_start: 0.9025 (m-80) cc_final: 0.8778 (m-80) REVERT: B 451 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8707 (pp20) REVERT: B 504 LEU cc_start: 0.9149 (mt) cc_final: 0.8775 (mt) REVERT: C 35 VAL cc_start: 0.7955 (p) cc_final: 0.7740 (p) REVERT: C 51 TYR cc_start: 0.6919 (t80) cc_final: 0.6676 (t80) REVERT: C 53 LEU cc_start: 0.9466 (mt) cc_final: 0.9140 (mt) REVERT: C 55 ASN cc_start: 0.9294 (m110) cc_final: 0.9064 (m-40) REVERT: C 351 PHE cc_start: 0.8966 (m-80) cc_final: 0.8629 (m-80) REVERT: C 353 LYS cc_start: 0.9471 (pptt) cc_final: 0.9045 (ptpp) REVERT: C 377 LEU cc_start: 0.9248 (mt) cc_final: 0.9003 (tt) REVERT: C 448 ASP cc_start: 0.9526 (t0) cc_final: 0.9079 (p0) REVERT: C 504 LEU cc_start: 0.8780 (mt) cc_final: 0.8553 (mt) REVERT: C 524 ILE cc_start: 0.8545 (mt) cc_final: 0.8285 (mt) REVERT: D 51 TYR cc_start: 0.7025 (t80) cc_final: 0.6584 (t80) REVERT: D 52 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8512 (tp30) REVERT: D 61 ARG cc_start: 0.9564 (ttp-110) cc_final: 0.9188 (ptp-110) REVERT: D 90 MET cc_start: 0.8719 (tpt) cc_final: 0.8517 (mmm) REVERT: D 342 GLN cc_start: 0.9158 (pp30) cc_final: 0.8079 (mm-40) REVERT: D 351 PHE cc_start: 0.9087 (m-80) cc_final: 0.8870 (m-80) REVERT: D 461 GLU cc_start: 0.7682 (pp20) cc_final: 0.7325 (pp20) REVERT: D 524 ILE cc_start: 0.8804 (mt) cc_final: 0.8256 (mt) REVERT: E 51 TYR cc_start: 0.6902 (t80) cc_final: 0.6181 (t80) REVERT: E 53 LEU cc_start: 0.9153 (mm) cc_final: 0.8882 (mm) REVERT: E 60 LYS cc_start: 0.9525 (mmtm) cc_final: 0.9180 (mmmt) REVERT: E 351 PHE cc_start: 0.9004 (m-80) cc_final: 0.8778 (m-80) REVERT: E 451 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8816 (pp20) REVERT: E 504 LEU cc_start: 0.9076 (mt) cc_final: 0.8643 (mt) REVERT: F 51 TYR cc_start: 0.6926 (t80) cc_final: 0.6661 (t80) REVERT: F 52 GLU cc_start: 0.8778 (pp20) cc_final: 0.8520 (pp20) REVERT: F 53 LEU cc_start: 0.9471 (mt) cc_final: 0.9166 (mt) REVERT: F 55 ASN cc_start: 0.9296 (m110) cc_final: 0.9058 (m-40) REVERT: F 326 LYS cc_start: 0.9311 (mttt) cc_final: 0.9091 (mtmt) REVERT: F 351 PHE cc_start: 0.8938 (m-80) cc_final: 0.8622 (m-80) REVERT: F 353 LYS cc_start: 0.9350 (pptt) cc_final: 0.8949 (ptpp) REVERT: F 377 LEU cc_start: 0.9245 (mt) cc_final: 0.8985 (tt) REVERT: F 448 ASP cc_start: 0.9463 (t0) cc_final: 0.9031 (p0) REVERT: F 504 LEU cc_start: 0.8780 (mt) cc_final: 0.8551 (mt) REVERT: F 524 ILE cc_start: 0.8535 (mt) cc_final: 0.8273 (mt) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.3684 time to fit residues: 228.2304 Evaluate side-chains 348 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 195 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 68 optimal weight: 30.0000 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 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 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** 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 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.163334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.152078 restraints weight = 180709.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.153017 restraints weight = 152918.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.153663 restraints weight = 131086.034| |-----------------------------------------------------------------------------| r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 1.1167 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= 0.175 Angle : 0.882 9.513 27396 Z= 0.467 Chirality : 0.054 0.471 3084 Planarity : 0.005 0.048 3570 Dihedral : 7.560 54.552 2730 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.19 % Favored : 85.87 % Rotamer: Outliers : 0.05 % Allowed : 2.30 % Favored : 97.66 % 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: -3.93 (0.14), residues: 2448 helix: -0.61 (0.18), residues: 696 sheet: -1.94 (0.27), residues: 312 loop : -4.06 (0.12), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 320 HIS 0.004 0.001 HIS C 407 PHE 0.047 0.002 PHE A 143 TYR 0.025 0.002 TYR E 566 ARG 0.013 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.05224 ( 600) hydrogen bonds : angle 6.25692 ( 1728) covalent geometry : bond 0.00367 (20346) covalent geometry : angle 0.88231 (27396) *********************** 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 408 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 407 time to evaluate : 2.047 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: A 51 TYR cc_start: 0.7464 (t80) cc_final: 0.6813 (t80) REVERT: A 342 GLN cc_start: 0.9276 (pp30) cc_final: 0.8495 (mp10) REVERT: A 351 PHE cc_start: 0.8988 (m-80) cc_final: 0.8729 (m-80) REVERT: A 504 LEU cc_start: 0.8929 (mt) cc_final: 0.8717 (mt) REVERT: A 524 ILE cc_start: 0.8889 (mt) cc_final: 0.8315 (mt) REVERT: A 557 ASN cc_start: 0.6230 (t0) cc_final: 0.5742 (t0) REVERT: B 51 TYR cc_start: 0.6771 (t80) cc_final: 0.6188 (t80) REVERT: B 52 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7368 (tm-30) REVERT: B 60 LYS cc_start: 0.9521 (mmpt) cc_final: 0.9278 (mmmt) REVERT: B 62 LEU cc_start: 0.9560 (mm) cc_final: 0.9358 (mm) REVERT: B 326 LYS cc_start: 0.8838 (ptpt) cc_final: 0.8629 (pttt) REVERT: B 342 GLN cc_start: 0.9433 (pp30) cc_final: 0.8417 (mm-40) REVERT: B 451 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8628 (pp20) REVERT: B 499 PHE cc_start: 0.8275 (m-10) cc_final: 0.7974 (m-10) REVERT: B 504 LEU cc_start: 0.9052 (mt) cc_final: 0.8795 (mt) REVERT: B 524 ILE cc_start: 0.8576 (mt) cc_final: 0.8203 (mt) REVERT: C 35 VAL cc_start: 0.8184 (p) cc_final: 0.7946 (p) REVERT: C 52 GLU cc_start: 0.8752 (pp20) cc_final: 0.8462 (pp20) REVERT: C 55 ASN cc_start: 0.8972 (m110) cc_final: 0.8609 (m110) REVERT: C 56 TYR cc_start: 0.8901 (t80) cc_final: 0.8604 (t80) REVERT: C 342 GLN cc_start: 0.9119 (pp30) cc_final: 0.8384 (mm-40) REVERT: C 351 PHE cc_start: 0.8917 (m-80) cc_final: 0.8625 (m-80) REVERT: C 353 LYS cc_start: 0.9451 (pptt) cc_final: 0.9005 (ptpp) REVERT: C 448 ASP cc_start: 0.9501 (t0) cc_final: 0.8952 (p0) REVERT: C 504 LEU cc_start: 0.8840 (mt) cc_final: 0.8600 (mt) REVERT: C 524 ILE cc_start: 0.8890 (mt) cc_final: 0.8486 (mt) REVERT: D 51 TYR cc_start: 0.7440 (t80) cc_final: 0.6869 (t80) REVERT: D 61 ARG cc_start: 0.9587 (ttp-110) cc_final: 0.9245 (ptp-110) REVERT: D 342 GLN cc_start: 0.9263 (pp30) cc_final: 0.8322 (mm-40) REVERT: D 351 PHE cc_start: 0.9136 (m-80) cc_final: 0.8805 (m-80) REVERT: D 461 GLU cc_start: 0.7633 (pp20) cc_final: 0.7223 (pp20) REVERT: D 504 LEU cc_start: 0.8933 (mt) cc_final: 0.8715 (mt) REVERT: D 524 ILE cc_start: 0.8883 (mt) cc_final: 0.8336 (mt) REVERT: D 557 ASN cc_start: 0.6287 (t0) cc_final: 0.5779 (t0) REVERT: E 51 TYR cc_start: 0.6750 (t80) cc_final: 0.6224 (t80) REVERT: E 52 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6739 (tm-30) REVERT: E 53 LEU cc_start: 0.9393 (mm) cc_final: 0.9038 (mm) REVERT: E 60 LYS cc_start: 0.9539 (mmtm) cc_final: 0.9304 (tppt) REVERT: E 326 LYS cc_start: 0.8800 (ptpt) cc_final: 0.8573 (pttt) REVERT: E 342 GLN cc_start: 0.9335 (pp30) cc_final: 0.8579 (mp-120) REVERT: E 351 PHE cc_start: 0.8916 (m-80) cc_final: 0.8710 (m-80) REVERT: E 451 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8637 (pp20) REVERT: E 499 PHE cc_start: 0.8230 (m-10) cc_final: 0.7929 (m-10) REVERT: E 504 LEU cc_start: 0.9000 (mt) cc_final: 0.8690 (mt) REVERT: E 524 ILE cc_start: 0.8556 (mt) cc_final: 0.8187 (mt) REVERT: F 35 VAL cc_start: 0.8157 (p) cc_final: 0.7931 (p) REVERT: F 52 GLU cc_start: 0.8895 (pp20) cc_final: 0.8293 (tp30) REVERT: F 56 TYR cc_start: 0.8863 (t80) cc_final: 0.8614 (t80) REVERT: F 342 GLN cc_start: 0.9054 (pp30) cc_final: 0.8383 (mm-40) REVERT: F 351 PHE cc_start: 0.8868 (m-80) cc_final: 0.8594 (m-80) REVERT: F 353 LYS cc_start: 0.9443 (pptt) cc_final: 0.8963 (ptpp) REVERT: F 448 ASP cc_start: 0.9460 (t0) cc_final: 0.8917 (p0) REVERT: F 504 LEU cc_start: 0.8861 (mt) cc_final: 0.8618 (mt) REVERT: F 524 ILE cc_start: 0.8887 (mt) cc_final: 0.8476 (mt) REVERT: F 557 ASN cc_start: 0.5900 (t0) cc_final: 0.5699 (t0) outliers start: 1 outliers final: 1 residues processed: 408 average time/residue: 0.3582 time to fit residues: 212.5682 Evaluate side-chains 343 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 224 optimal weight: 30.0000 chunk 174 optimal weight: 0.9990 chunk 137 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** 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 455 ASN ** 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 394 ASN ** 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 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.160607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.149317 restraints weight = 181650.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.150311 restraints weight = 154591.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.150864 restraints weight = 133182.915| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 1.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 20346 Z= 0.185 Angle : 0.894 11.019 27396 Z= 0.470 Chirality : 0.053 0.415 3084 Planarity : 0.005 0.059 3570 Dihedral : 7.527 50.901 2730 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 24.25 Ramachandran Plot: Outliers : 1.18 % Allowed : 13.77 % Favored : 85.05 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -3.83 (0.15), residues: 2448 helix: -0.60 (0.19), residues: 684 sheet: -1.82 (0.29), residues: 282 loop : -3.92 (0.12), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 320 HIS 0.003 0.001 HIS C 407 PHE 0.048 0.002 PHE B 143 TYR 0.027 0.002 TYR C 566 ARG 0.013 0.001 ARG F 54 Details of bonding type rmsd hydrogen bonds : bond 0.04999 ( 600) hydrogen bonds : angle 6.36960 ( 1728) covalent geometry : bond 0.00389 (20346) covalent geometry : angle 0.89420 (27396) *********************** 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 399 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 2.242 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: A 41 GLN cc_start: 0.9147 (mp10) cc_final: 0.8945 (mp10) REVERT: A 51 TYR cc_start: 0.7548 (t80) cc_final: 0.6856 (t80) REVERT: A 55 ASN cc_start: 0.9422 (m-40) cc_final: 0.9209 (m-40) REVERT: A 342 GLN cc_start: 0.9178 (pp30) cc_final: 0.8465 (mp10) REVERT: A 351 PHE cc_start: 0.9059 (m-80) cc_final: 0.8825 (m-80) REVERT: A 504 LEU cc_start: 0.8959 (mt) cc_final: 0.8733 (mt) REVERT: A 524 ILE cc_start: 0.8924 (mt) cc_final: 0.8268 (mt) REVERT: A 557 ASN cc_start: 0.6329 (t0) cc_final: 0.5973 (m-40) REVERT: B 51 TYR cc_start: 0.7081 (t80) cc_final: 0.6536 (t80) REVERT: B 52 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7417 (tm-30) REVERT: B 87 ILE cc_start: 0.9144 (mp) cc_final: 0.8881 (mp) REVERT: B 351 PHE cc_start: 0.9011 (m-80) cc_final: 0.8810 (m-80) REVERT: B 412 MET cc_start: 0.3936 (mmp) cc_final: 0.3618 (mmm) REVERT: B 451 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8567 (pp20) REVERT: B 466 ARG cc_start: 0.8143 (tmm160) cc_final: 0.7796 (tmm160) REVERT: B 498 ASP cc_start: 0.9270 (t70) cc_final: 0.8925 (t0) REVERT: B 504 LEU cc_start: 0.9053 (mt) cc_final: 0.8799 (mt) REVERT: B 524 ILE cc_start: 0.8650 (mt) cc_final: 0.8194 (mt) REVERT: C 35 VAL cc_start: 0.8355 (p) cc_final: 0.8114 (p) REVERT: C 51 TYR cc_start: 0.7122 (t80) cc_final: 0.6540 (t80) REVERT: C 52 GLU cc_start: 0.8892 (pp20) cc_final: 0.8619 (tp30) REVERT: C 351 PHE cc_start: 0.8866 (m-80) cc_final: 0.8564 (m-80) REVERT: C 353 LYS cc_start: 0.9448 (pptt) cc_final: 0.9003 (ptpp) REVERT: C 377 LEU cc_start: 0.9292 (mt) cc_final: 0.8987 (tt) REVERT: C 504 LEU cc_start: 0.8908 (mt) cc_final: 0.8675 (mt) REVERT: C 524 ILE cc_start: 0.8868 (mt) cc_final: 0.8441 (mt) REVERT: D 51 TYR cc_start: 0.7621 (t80) cc_final: 0.7076 (t80) REVERT: D 61 ARG cc_start: 0.9565 (ttp-110) cc_final: 0.9210 (ptp-110) REVERT: D 342 GLN cc_start: 0.9421 (pp30) cc_final: 0.8647 (mm-40) REVERT: D 351 PHE cc_start: 0.9157 (m-80) cc_final: 0.8804 (m-80) REVERT: D 461 GLU cc_start: 0.7856 (pp20) cc_final: 0.7477 (pp20) REVERT: D 504 LEU cc_start: 0.8989 (mt) cc_final: 0.8782 (mt) REVERT: D 524 ILE cc_start: 0.8940 (mt) cc_final: 0.8307 (mt) REVERT: D 557 ASN cc_start: 0.6662 (t0) cc_final: 0.6100 (m-40) REVERT: E 51 TYR cc_start: 0.7012 (t80) cc_final: 0.6708 (t80) REVERT: E 52 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6952 (tm-30) REVERT: E 60 LYS cc_start: 0.9575 (mmtm) cc_final: 0.9174 (mmmt) REVERT: E 351 PHE cc_start: 0.8962 (m-80) cc_final: 0.8749 (m-80) REVERT: E 377 LEU cc_start: 0.9114 (mt) cc_final: 0.8875 (mt) REVERT: E 451 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8894 (pp20) REVERT: E 498 ASP cc_start: 0.9249 (t70) cc_final: 0.8906 (t0) REVERT: E 504 LEU cc_start: 0.8985 (mt) cc_final: 0.8695 (mt) REVERT: E 524 ILE cc_start: 0.8642 (mt) cc_final: 0.8191 (mt) REVERT: F 35 VAL cc_start: 0.8295 (p) cc_final: 0.8085 (p) REVERT: F 51 TYR cc_start: 0.7280 (t80) cc_final: 0.6474 (t80) REVERT: F 53 LEU cc_start: 0.9696 (mt) cc_final: 0.9333 (mm) REVERT: F 351 PHE cc_start: 0.8818 (m-80) cc_final: 0.8535 (m-80) REVERT: F 353 LYS cc_start: 0.9425 (pptt) cc_final: 0.8969 (ptpp) REVERT: F 377 LEU cc_start: 0.9388 (mt) cc_final: 0.9022 (tt) REVERT: F 504 LEU cc_start: 0.8933 (mt) cc_final: 0.8700 (mt) REVERT: F 524 ILE cc_start: 0.8874 (mt) cc_final: 0.8446 (mt) REVERT: F 557 ASN cc_start: 0.6058 (t0) cc_final: 0.5227 (t0) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.3551 time to fit residues: 206.8831 Evaluate side-chains 334 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 186 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 169 optimal weight: 6.9990 chunk 219 optimal weight: 30.0000 chunk 156 optimal weight: 4.9990 chunk 162 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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** ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN ** D 394 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** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.159002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.147863 restraints weight = 182027.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.148902 restraints weight = 153156.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.149589 restraints weight = 132197.941| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5846 moved from start: 1.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20346 Z= 0.186 Angle : 0.886 10.108 27396 Z= 0.466 Chirality : 0.053 0.440 3084 Planarity : 0.006 0.064 3570 Dihedral : 7.655 52.062 2730 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 23.60 Ramachandran Plot: Outliers : 1.14 % Allowed : 14.83 % Favored : 84.03 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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 (0.14), residues: 2448 helix: -0.74 (0.19), residues: 690 sheet: -1.45 (0.28), residues: 294 loop : -4.04 (0.12), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 320 HIS 0.003 0.001 HIS F 407 PHE 0.040 0.002 PHE B 143 TYR 0.022 0.002 TYR B 532 ARG 0.008 0.001 ARG A 380 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 600) hydrogen bonds : angle 6.36274 ( 1728) covalent geometry : bond 0.00382 (20346) covalent geometry : angle 0.88599 (27396) *********************** 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 395 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 2.100 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: A 51 TYR cc_start: 0.7626 (t80) cc_final: 0.7124 (t80) REVERT: A 55 ASN cc_start: 0.9483 (m-40) cc_final: 0.9232 (m-40) REVERT: A 56 TYR cc_start: 0.9248 (t80) cc_final: 0.8944 (t80) REVERT: A 342 GLN cc_start: 0.8984 (pp30) cc_final: 0.8347 (mp10) REVERT: A 351 PHE cc_start: 0.9009 (m-80) cc_final: 0.8801 (m-80) REVERT: A 504 LEU cc_start: 0.9020 (mt) cc_final: 0.8798 (mt) REVERT: A 524 ILE cc_start: 0.9018 (mt) cc_final: 0.8604 (mt) REVERT: A 525 ILE cc_start: 0.8253 (mt) cc_final: 0.7844 (mm) REVERT: A 557 ASN cc_start: 0.6435 (t0) cc_final: 0.6179 (m-40) REVERT: B 51 TYR cc_start: 0.6935 (t80) cc_final: 0.6709 (t80) REVERT: B 52 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7288 (tm-30) REVERT: B 342 GLN cc_start: 0.8952 (pm20) cc_final: 0.8238 (mp10) REVERT: B 351 PHE cc_start: 0.8880 (m-80) cc_final: 0.8663 (m-80) REVERT: B 394 ASN cc_start: 0.7310 (t0) cc_final: 0.6467 (t0) REVERT: B 451 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8646 (pp20) REVERT: B 466 ARG cc_start: 0.8295 (tmm160) cc_final: 0.7925 (tmm160) REVERT: B 504 LEU cc_start: 0.8896 (mt) cc_final: 0.8582 (mt) REVERT: B 524 ILE cc_start: 0.8587 (mt) cc_final: 0.7924 (mt) REVERT: C 52 GLU cc_start: 0.8854 (pp20) cc_final: 0.8552 (tp30) REVERT: C 62 LEU cc_start: 0.9492 (mm) cc_final: 0.9209 (mm) REVERT: C 351 PHE cc_start: 0.8734 (m-80) cc_final: 0.8455 (m-80) REVERT: C 353 LYS cc_start: 0.9372 (pptt) cc_final: 0.8958 (ptpp) REVERT: C 461 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8481 (tm-30) REVERT: C 504 LEU cc_start: 0.8866 (mt) cc_final: 0.8615 (mt) REVERT: C 524 ILE cc_start: 0.8703 (mt) cc_final: 0.8137 (mt) REVERT: C 525 ILE cc_start: 0.8480 (mt) cc_final: 0.7898 (mm) REVERT: D 51 TYR cc_start: 0.7602 (t80) cc_final: 0.7102 (t80) REVERT: D 55 ASN cc_start: 0.9409 (m-40) cc_final: 0.9111 (m-40) REVERT: D 56 TYR cc_start: 0.9293 (t80) cc_final: 0.9075 (t80) REVERT: D 342 GLN cc_start: 0.9215 (pp30) cc_final: 0.8361 (mm-40) REVERT: D 351 PHE cc_start: 0.9124 (m-80) cc_final: 0.8823 (m-80) REVERT: D 461 GLU cc_start: 0.7758 (pp20) cc_final: 0.7466 (pp20) REVERT: D 504 LEU cc_start: 0.8752 (mt) cc_final: 0.8537 (mt) REVERT: D 524 ILE cc_start: 0.9001 (mt) cc_final: 0.8585 (mt) REVERT: D 525 ILE cc_start: 0.8267 (mt) cc_final: 0.7858 (mm) REVERT: D 557 ASN cc_start: 0.5722 (t0) cc_final: 0.5444 (m-40) REVERT: E 60 LYS cc_start: 0.9635 (mmtm) cc_final: 0.9426 (tppt) REVERT: E 62 LEU cc_start: 0.9596 (mm) cc_final: 0.9376 (mm) REVERT: E 342 GLN cc_start: 0.9415 (pp30) cc_final: 0.8543 (mm-40) REVERT: E 351 PHE cc_start: 0.8846 (m-80) cc_final: 0.8630 (m-80) REVERT: E 380 ARG cc_start: 0.8608 (tmm160) cc_final: 0.8078 (tmm160) REVERT: E 394 ASN cc_start: 0.7404 (t0) cc_final: 0.6766 (t0) REVERT: E 451 GLU cc_start: 0.9359 (tm-30) cc_final: 0.9090 (pp20) REVERT: E 466 ARG cc_start: 0.8075 (tmm160) cc_final: 0.7728 (tmm160) REVERT: E 504 LEU cc_start: 0.8863 (mt) cc_final: 0.8563 (mt) REVERT: E 524 ILE cc_start: 0.8573 (mt) cc_final: 0.7910 (mt) REVERT: F 51 TYR cc_start: 0.6904 (t80) cc_final: 0.6485 (t80) REVERT: F 62 LEU cc_start: 0.9495 (mm) cc_final: 0.9294 (mm) REVERT: F 351 PHE cc_start: 0.8647 (m-80) cc_final: 0.8402 (m-80) REVERT: F 353 LYS cc_start: 0.9335 (pptt) cc_final: 0.8916 (ptpp) REVERT: F 461 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8480 (tm-30) REVERT: F 504 LEU cc_start: 0.8870 (mt) cc_final: 0.8620 (mt) REVERT: F 524 ILE cc_start: 0.8740 (mt) cc_final: 0.8173 (mt) REVERT: F 525 ILE cc_start: 0.8505 (mt) cc_final: 0.7927 (mm) REVERT: F 557 ASN cc_start: 0.6247 (t0) cc_final: 0.5896 (m-40) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.3566 time to fit residues: 204.7970 Evaluate side-chains 335 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 142 optimal weight: 0.0870 chunk 185 optimal weight: 9.9990 chunk 106 optimal weight: 0.0040 chunk 31 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN A 279 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** 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 381 GLN ** 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 58 GLN D 279 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 453 ASN E 81 ASN E 279 ASN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.163827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.152540 restraints weight = 179918.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.153554 restraints weight = 149671.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.154178 restraints weight = 127021.327| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 1.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20346 Z= 0.154 Angle : 0.851 11.040 27396 Z= 0.446 Chirality : 0.050 0.284 3084 Planarity : 0.005 0.064 3570 Dihedral : 7.078 53.806 2730 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 1.27 % Allowed : 12.58 % Favored : 86.15 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -3.63 (0.15), residues: 2448 helix: -0.58 (0.19), residues: 690 sheet: -1.38 (0.29), residues: 294 loop : -3.81 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 76 HIS 0.004 0.001 HIS A 345 PHE 0.031 0.001 PHE B 143 TYR 0.018 0.002 TYR F 411 ARG 0.013 0.001 ARG C 61 Details of bonding type rmsd hydrogen bonds : bond 0.04888 ( 600) hydrogen bonds : angle 5.94671 ( 1728) covalent geometry : bond 0.00317 (20346) covalent geometry : angle 0.85073 (27396) *********************** 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 405 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 2.133 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: A 51 TYR cc_start: 0.7549 (t80) cc_final: 0.7123 (t80) REVERT: A 55 ASN cc_start: 0.9361 (m-40) cc_final: 0.9055 (m-40) REVERT: A 90 MET cc_start: 0.7083 (mmm) cc_final: 0.6761 (mmm) REVERT: A 342 GLN cc_start: 0.9097 (pp30) cc_final: 0.8510 (mp10) REVERT: A 351 PHE cc_start: 0.8954 (m-80) cc_final: 0.8709 (m-80) REVERT: A 394 ASN cc_start: 0.5849 (m110) cc_final: 0.5605 (m110) REVERT: A 497 ASN cc_start: 0.9330 (m-40) cc_final: 0.8741 (m110) REVERT: A 504 LEU cc_start: 0.8880 (mt) cc_final: 0.8432 (mt) REVERT: A 524 ILE cc_start: 0.8943 (mt) cc_final: 0.8559 (mt) REVERT: A 525 ILE cc_start: 0.8188 (mt) cc_final: 0.7884 (mm) REVERT: A 557 ASN cc_start: 0.5465 (t0) cc_final: 0.5139 (m-40) REVERT: B 51 TYR cc_start: 0.7162 (t80) cc_final: 0.6918 (t80) REVERT: B 52 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7612 (tm-30) REVERT: B 54 ARG cc_start: 0.9243 (mtm-85) cc_final: 0.8734 (mtm-85) REVERT: B 62 LEU cc_start: 0.9553 (mm) cc_final: 0.9249 (mm) REVERT: B 87 ILE cc_start: 0.8867 (mp) cc_final: 0.8474 (mp) REVERT: B 342 GLN cc_start: 0.8989 (pm20) cc_final: 0.8491 (mp10) REVERT: B 351 PHE cc_start: 0.8825 (m-80) cc_final: 0.8587 (m-80) REVERT: B 381 GLN cc_start: 0.6110 (pt0) cc_final: 0.5649 (tt0) REVERT: B 451 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8434 (pp20) REVERT: B 497 ASN cc_start: 0.9102 (m-40) cc_final: 0.8563 (m-40) REVERT: B 504 LEU cc_start: 0.8926 (mt) cc_final: 0.8690 (mt) REVERT: B 524 ILE cc_start: 0.8620 (mt) cc_final: 0.7970 (mt) REVERT: C 52 GLU cc_start: 0.8859 (pp20) cc_final: 0.8322 (tm-30) REVERT: C 62 LEU cc_start: 0.9536 (mm) cc_final: 0.9123 (mm) REVERT: C 342 GLN cc_start: 0.8605 (pm20) cc_final: 0.7953 (mm-40) REVERT: C 351 PHE cc_start: 0.8483 (m-80) cc_final: 0.8208 (m-80) REVERT: C 353 LYS cc_start: 0.9252 (pptt) cc_final: 0.8912 (ptpp) REVERT: C 497 ASN cc_start: 0.9102 (m-40) cc_final: 0.8812 (m-40) REVERT: C 504 LEU cc_start: 0.8682 (mt) cc_final: 0.8004 (mt) REVERT: C 524 ILE cc_start: 0.8594 (mt) cc_final: 0.7892 (mt) REVERT: C 525 ILE cc_start: 0.8451 (mt) cc_final: 0.7945 (mm) REVERT: D 51 TYR cc_start: 0.7476 (t80) cc_final: 0.7156 (t80) REVERT: D 55 ASN cc_start: 0.9383 (m-40) cc_final: 0.9062 (m-40) REVERT: D 342 GLN cc_start: 0.9298 (pp30) cc_final: 0.8818 (mp10) REVERT: D 351 PHE cc_start: 0.9027 (m-80) cc_final: 0.8735 (m-80) REVERT: D 497 ASN cc_start: 0.9344 (m-40) cc_final: 0.8757 (m110) REVERT: D 504 LEU cc_start: 0.8511 (mt) cc_final: 0.7946 (mt) REVERT: D 524 ILE cc_start: 0.8915 (mt) cc_final: 0.8540 (mt) REVERT: D 557 ASN cc_start: 0.5581 (t0) cc_final: 0.5293 (m-40) REVERT: E 53 LEU cc_start: 0.9397 (mm) cc_final: 0.8961 (mm) REVERT: E 60 LYS cc_start: 0.9525 (mmtm) cc_final: 0.9242 (mmmt) REVERT: E 62 LEU cc_start: 0.9536 (mm) cc_final: 0.9263 (mm) REVERT: E 342 GLN cc_start: 0.9385 (pp30) cc_final: 0.8339 (mp10) REVERT: E 351 PHE cc_start: 0.8752 (m-80) cc_final: 0.8505 (m-80) REVERT: E 497 ASN cc_start: 0.9089 (m-40) cc_final: 0.8560 (m110) REVERT: E 504 LEU cc_start: 0.8927 (mt) cc_final: 0.8610 (mt) REVERT: E 524 ILE cc_start: 0.8615 (mt) cc_final: 0.7974 (mt) REVERT: F 60 LYS cc_start: 0.9416 (mmpt) cc_final: 0.9211 (mmmt) REVERT: F 62 LEU cc_start: 0.9578 (mm) cc_final: 0.9133 (mm) REVERT: F 351 PHE cc_start: 0.8431 (m-80) cc_final: 0.8184 (m-80) REVERT: F 353 LYS cc_start: 0.9225 (pptt) cc_final: 0.8881 (ptpp) REVERT: F 497 ASN cc_start: 0.9116 (m-40) cc_final: 0.8861 (m-40) REVERT: F 504 LEU cc_start: 0.8707 (mt) cc_final: 0.8033 (mt) REVERT: F 524 ILE cc_start: 0.8604 (mt) cc_final: 0.7923 (mt) REVERT: F 525 ILE cc_start: 0.8449 (mt) cc_final: 0.7948 (mm) REVERT: F 557 ASN cc_start: 0.6280 (t0) cc_final: 0.5933 (m-40) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.3683 time to fit residues: 214.4992 Evaluate side-chains 328 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 31 optimal weight: 30.0000 chunk 86 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 171 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 233 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 overall best weight: 3.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** 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 376 GLN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 376 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.161182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.149950 restraints weight = 181232.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.150950 restraints weight = 150439.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.151899 restraints weight = 127220.686| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 1.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20346 Z= 0.168 Angle : 0.898 12.027 27396 Z= 0.471 Chirality : 0.052 0.267 3084 Planarity : 0.005 0.066 3570 Dihedral : 7.084 54.987 2730 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 1.23 % Allowed : 14.17 % Favored : 84.60 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.45 % 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: -3.67 (0.15), residues: 2448 helix: -0.71 (0.19), residues: 690 sheet: -1.30 (0.29), residues: 294 loop : -3.81 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 76 HIS 0.006 0.001 HIS B 345 PHE 0.037 0.002 PHE B 167 TYR 0.036 0.002 TYR F 532 ARG 0.007 0.001 ARG D 535 Details of bonding type rmsd hydrogen bonds : bond 0.04933 ( 600) hydrogen bonds : angle 6.06710 ( 1728) covalent geometry : bond 0.00352 (20346) covalent geometry : angle 0.89769 (27396) ********************** 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 378 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 2.295 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 51 TYR cc_start: 0.7552 (t80) cc_final: 0.7176 (t80) REVERT: A 55 ASN cc_start: 0.9328 (m-40) cc_final: 0.9042 (m-40) REVERT: A 342 GLN cc_start: 0.9237 (pp30) cc_final: 0.8768 (mp10) REVERT: A 351 PHE cc_start: 0.9042 (m-80) cc_final: 0.8730 (m-80) REVERT: A 445 GLU cc_start: 0.8714 (pp20) cc_final: 0.8280 (pm20) REVERT: A 497 ASN cc_start: 0.9442 (m-40) cc_final: 0.8857 (m110) REVERT: A 504 LEU cc_start: 0.8798 (mt) cc_final: 0.8485 (mt) REVERT: A 524 ILE cc_start: 0.8904 (mt) cc_final: 0.8416 (mt) REVERT: A 525 ILE cc_start: 0.8386 (mt) cc_final: 0.8133 (mm) REVERT: B 51 TYR cc_start: 0.7001 (t80) cc_final: 0.6723 (t80) REVERT: B 52 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 54 ARG cc_start: 0.9125 (mtm-85) cc_final: 0.8732 (mtm-85) REVERT: B 62 LEU cc_start: 0.9655 (mm) cc_final: 0.9331 (mm) REVERT: B 87 ILE cc_start: 0.8783 (mp) cc_final: 0.8430 (mp) REVERT: B 90 MET cc_start: 0.6919 (mmm) cc_final: 0.6539 (mmm) REVERT: B 342 GLN cc_start: 0.9227 (pm20) cc_final: 0.8723 (mm-40) REVERT: B 351 PHE cc_start: 0.8980 (m-80) cc_final: 0.8658 (m-80) REVERT: B 451 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8814 (pp20) REVERT: B 455 ASN cc_start: 0.5694 (t0) cc_final: 0.5413 (t0) REVERT: B 497 ASN cc_start: 0.9250 (m-40) cc_final: 0.8715 (m110) REVERT: B 499 PHE cc_start: 0.8807 (m-80) cc_final: 0.8519 (m-80) REVERT: B 504 LEU cc_start: 0.8958 (mt) cc_final: 0.8726 (mt) REVERT: B 524 ILE cc_start: 0.8732 (mt) cc_final: 0.8028 (mt) REVERT: C 60 LYS cc_start: 0.9494 (mmpt) cc_final: 0.9175 (mmmt) REVERT: C 62 LEU cc_start: 0.9552 (mm) cc_final: 0.9240 (mm) REVERT: C 351 PHE cc_start: 0.8681 (m-80) cc_final: 0.8306 (m-80) REVERT: C 353 LYS cc_start: 0.9316 (pptt) cc_final: 0.8959 (ptpp) REVERT: C 411 TYR cc_start: 0.6291 (m-10) cc_final: 0.6014 (m-10) REVERT: C 497 ASN cc_start: 0.9265 (m-40) cc_final: 0.8839 (m-40) REVERT: C 498 ASP cc_start: 0.9232 (t70) cc_final: 0.8906 (t0) REVERT: C 504 LEU cc_start: 0.8918 (mt) cc_final: 0.8493 (mt) REVERT: C 524 ILE cc_start: 0.8705 (mt) cc_final: 0.8118 (mt) REVERT: C 525 ILE cc_start: 0.8641 (mt) cc_final: 0.8126 (mm) REVERT: D 51 TYR cc_start: 0.7488 (t80) cc_final: 0.7160 (t80) REVERT: D 55 ASN cc_start: 0.9398 (m-40) cc_final: 0.9077 (m-40) REVERT: D 61 ARG cc_start: 0.9324 (ttm110) cc_final: 0.8912 (ptp-110) REVERT: D 342 GLN cc_start: 0.9320 (pp30) cc_final: 0.8792 (mp10) REVERT: D 351 PHE cc_start: 0.9068 (m-80) cc_final: 0.8817 (m-80) REVERT: D 497 ASN cc_start: 0.9420 (m-40) cc_final: 0.8827 (m110) REVERT: D 504 LEU cc_start: 0.8626 (mt) cc_final: 0.8297 (mt) REVERT: D 524 ILE cc_start: 0.8905 (mt) cc_final: 0.8390 (mt) REVERT: D 525 ILE cc_start: 0.8451 (mt) cc_final: 0.8168 (mm) REVERT: D 532 TYR cc_start: 0.7426 (t80) cc_final: 0.7192 (t80) REVERT: E 60 LYS cc_start: 0.9658 (mmtm) cc_final: 0.9335 (mmmt) REVERT: E 62 LEU cc_start: 0.9585 (mm) cc_final: 0.9307 (mm) REVERT: E 351 PHE cc_start: 0.8930 (m-80) cc_final: 0.8603 (m-80) REVERT: E 380 ARG cc_start: 0.8640 (tmm160) cc_final: 0.8395 (ttp80) REVERT: E 497 ASN cc_start: 0.9159 (m-40) cc_final: 0.8601 (m110) REVERT: E 499 PHE cc_start: 0.8761 (m-80) cc_final: 0.8498 (m-80) REVERT: E 504 LEU cc_start: 0.8996 (mt) cc_final: 0.8739 (mt) REVERT: E 524 ILE cc_start: 0.8785 (mt) cc_final: 0.8073 (mt) REVERT: F 51 TYR cc_start: 0.6722 (t80) cc_final: 0.6174 (t80) REVERT: F 60 LYS cc_start: 0.9506 (mmpt) cc_final: 0.9264 (mmmt) REVERT: F 62 LEU cc_start: 0.9559 (mm) cc_final: 0.9169 (mm) REVERT: F 351 PHE cc_start: 0.8625 (m-80) cc_final: 0.8297 (m-80) REVERT: F 353 LYS cc_start: 0.9288 (pptt) cc_final: 0.8926 (ptpp) REVERT: F 411 TYR cc_start: 0.6195 (m-10) cc_final: 0.5951 (m-10) REVERT: F 497 ASN cc_start: 0.9286 (m-40) cc_final: 0.8853 (m-40) REVERT: F 498 ASP cc_start: 0.9216 (t70) cc_final: 0.8901 (t0) REVERT: F 504 LEU cc_start: 0.8973 (mt) cc_final: 0.8551 (mt) REVERT: F 524 ILE cc_start: 0.8694 (mt) cc_final: 0.8128 (mt) REVERT: F 525 ILE cc_start: 0.8626 (mt) cc_final: 0.8113 (mm) outliers start: 1 outliers final: 0 residues processed: 378 average time/residue: 0.3714 time to fit residues: 203.4537 Evaluate side-chains 321 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 170 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 234 optimal weight: 2.9990 chunk 173 optimal weight: 30.0000 chunk 36 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 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 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 394 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** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.161117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.149756 restraints weight = 181772.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.150800 restraints weight = 151592.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.151613 restraints weight = 129105.217| |-----------------------------------------------------------------------------| r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5827 moved from start: 1.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20346 Z= 0.157 Angle : 0.873 13.601 27396 Z= 0.458 Chirality : 0.051 0.257 3084 Planarity : 0.005 0.058 3570 Dihedral : 7.013 54.694 2730 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 1.23 % Allowed : 14.22 % Favored : 84.56 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -3.64 (0.15), residues: 2448 helix: -0.63 (0.19), residues: 678 sheet: -1.45 (0.29), residues: 306 loop : -3.77 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 320 HIS 0.002 0.001 HIS D 171 PHE 0.032 0.002 PHE E 167 TYR 0.033 0.002 TYR B 411 ARG 0.015 0.001 ARG D 535 Details of bonding type rmsd hydrogen bonds : bond 0.04717 ( 600) hydrogen bonds : angle 5.99362 ( 1728) covalent geometry : bond 0.00324 (20346) covalent geometry : angle 0.87298 (27396) =============================================================================== Job complete usr+sys time: 7092.18 seconds wall clock time: 123 minutes 43.12 seconds (7423.12 seconds total)