Starting phenix.real_space_refine on Sun Aug 24 11:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5li4_4052/08_2025/5li4_4052.cif Found real_map, /net/cci-nas-00/data/ceres_data/5li4_4052/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/5li4_4052/08_2025/5li4_4052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5li4_4052/08_2025/5li4_4052.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5li4_4052/08_2025/5li4_4052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5li4_4052/08_2025/5li4_4052.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 2.64, per 1000 atoms: 0.13 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: 1.34 Conformation dependent library (CDL) restraints added in 721.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.53 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: 2.86 Time building geometry restraints manager: 1.69 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.870 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- 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 : 93.12 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG D 355 TYR 0.236 0.016 TYR A 444 PHE 0.099 0.015 PHE C 351 TRP 0.151 0.053 TRP D 320 HIS 0.009 0.002 HIS F 345 Details of bonding type rmsd covalent geometry : bond 0.05290 (20346) covalent geometry : angle 3.06564 (27396) hydrogen bonds : bond 0.21354 ( 600) hydrogen bonds : angle 10.27849 ( 1728) *********************** 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 : 0.660 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: A 39 ILE cc_start: 0.5185 (pt) cc_final: 0.4352 (pt) REVERT: A 50 VAL cc_start: 0.7572 (t) cc_final: 0.7143 (t) REVERT: B 39 ILE cc_start: 0.5546 (pt) cc_final: 0.5195 (pt) REVERT: B 153 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.5864 (tp) REVERT: B 362 MET cc_start: 0.4608 (pmm) cc_final: 0.4174 (tmm) REVERT: B 450 ASP cc_start: 0.6105 (p0) cc_final: 0.5891 (m-30) REVERT: C 39 ILE cc_start: 0.5845 (pt) cc_final: 0.5604 (pt) REVERT: C 362 MET cc_start: 0.5508 (pmm) cc_final: 0.4104 (tmm) REVERT: C 576 VAL cc_start: 0.5496 (t) cc_final: 0.5287 (p) REVERT: D 39 ILE cc_start: 0.5158 (pt) cc_final: 0.4345 (pt) REVERT: D 50 VAL cc_start: 0.7567 (t) cc_final: 0.7144 (t) REVERT: E 39 ILE cc_start: 0.5540 (pt) cc_final: 0.5105 (pt) REVERT: E 153 ILE cc_start: 0.6447 (OUTLIER) cc_final: 0.5863 (tp) REVERT: E 362 MET cc_start: 0.4609 (pmm) cc_final: 0.4138 (tmm) REVERT: E 450 ASP cc_start: 0.6113 (p0) cc_final: 0.5858 (m-30) REVERT: F 39 ILE cc_start: 0.5837 (pt) cc_final: 0.5605 (pt) REVERT: F 362 MET cc_start: 0.5420 (pmm) cc_final: 0.4104 (tmm) REVERT: F 576 VAL cc_start: 0.5558 (t) cc_final: 0.5343 (p) outliers start: 64 outliers final: 26 residues processed: 624 average time/residue: 0.1581 time to fit residues: 141.5075 Evaluate side-chains 380 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 352 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 HIS A 530 GLN B 55 ASN B 58 GLN B 176 GLN B 342 GLN B 406 ASN B 407 HIS B 530 GLN C 55 ASN C 58 GLN C 176 GLN C 342 GLN 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 E 406 ASN E 407 HIS E 530 GLN F 55 ASN F 58 GLN F 176 GLN F 342 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.169339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.158234 restraints weight = 180724.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.159185 restraints weight = 148625.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.159653 restraints weight = 126726.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.160254 restraints weight = 115276.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.160902 restraints weight = 104974.877| |-----------------------------------------------------------------------------| r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5561 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20346 Z= 0.278 Angle : 1.188 9.538 27396 Z= 0.637 Chirality : 0.067 0.421 3084 Planarity : 0.007 0.091 3570 Dihedral : 10.030 57.557 2730 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 29.89 Ramachandran Plot: Outliers : 1.23 % Allowed : 14.95 % Favored : 83.82 % Rotamer: Outliers : 0.92 % Allowed : 6.89 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 11.11 % Twisted General : 1.72 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.31 (0.13), residues: 2448 helix: -1.30 (0.18), residues: 684 sheet: -1.60 (0.23), residues: 390 loop : -4.34 (0.11), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 355 TYR 0.021 0.003 TYR E 112 PHE 0.031 0.003 PHE D 143 TRP 0.021 0.005 TRP B 76 HIS 0.007 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00589 (20346) covalent geometry : angle 1.18750 (27396) hydrogen bonds : bond 0.07399 ( 600) hydrogen bonds : angle 7.39603 ( 1728) *********************** 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 497 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 477 time to evaluate : 0.784 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 49 THR cc_start: 0.8293 (m) cc_final: 0.7985 (t) REVERT: A 76 TRP cc_start: 0.7793 (t60) cc_final: 0.6745 (t60) REVERT: A 114 ASN cc_start: 0.8933 (t0) cc_final: 0.8577 (m-40) REVERT: A 524 ILE cc_start: 0.7808 (mt) cc_final: 0.7447 (mt) REVERT: B 49 THR cc_start: 0.8241 (m) cc_final: 0.7684 (t) REVERT: B 76 TRP cc_start: 0.7276 (t60) cc_final: 0.6679 (t60) REVERT: B 88 LEU cc_start: 0.9565 (mt) cc_final: 0.9167 (mt) REVERT: B 342 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8436 (mm110) REVERT: B 417 LEU cc_start: 0.9655 (mt) cc_final: 0.9428 (pp) REVERT: B 504 LEU cc_start: 0.8603 (mt) cc_final: 0.8335 (mt) REVERT: B 524 ILE cc_start: 0.8113 (mt) cc_final: 0.7720 (mt) REVERT: C 35 VAL cc_start: 0.9107 (m) cc_final: 0.8781 (p) REVERT: C 49 THR cc_start: 0.8954 (m) cc_final: 0.8376 (t) REVERT: C 51 TYR cc_start: 0.6830 (t80) cc_final: 0.6484 (t80) REVERT: C 53 LEU cc_start: 0.9217 (mt) cc_final: 0.8658 (mm) REVERT: C 114 ASN cc_start: 0.8899 (t0) cc_final: 0.8688 (m-40) REVERT: C 411 TYR cc_start: 0.6656 (m-80) cc_final: 0.6079 (m-10) REVERT: C 417 LEU cc_start: 0.9634 (mt) cc_final: 0.9359 (pp) REVERT: C 452 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6353 (pp) REVERT: C 504 LEU cc_start: 0.8801 (mt) cc_final: 0.8540 (mt) REVERT: C 505 LYS cc_start: 0.8527 (tptt) cc_final: 0.8318 (mttt) REVERT: C 524 ILE cc_start: 0.7703 (mt) cc_final: 0.7295 (mt) REVERT: D 49 THR cc_start: 0.8286 (m) cc_final: 0.7974 (t) REVERT: D 76 TRP cc_start: 0.7787 (t60) cc_final: 0.6735 (t60) REVERT: D 114 ASN cc_start: 0.8965 (t0) cc_final: 0.8601 (m-40) REVERT: D 417 LEU cc_start: 0.9645 (mt) cc_final: 0.9445 (pp) REVERT: D 524 ILE cc_start: 0.7826 (mt) cc_final: 0.7472 (mt) REVERT: E 49 THR cc_start: 0.8300 (m) cc_final: 0.7720 (t) REVERT: E 76 TRP cc_start: 0.7248 (t60) cc_final: 0.6660 (t60) REVERT: E 88 LEU cc_start: 0.9559 (mt) cc_final: 0.9159 (mt) REVERT: E 342 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8553 (mm110) REVERT: E 417 LEU cc_start: 0.9657 (mt) cc_final: 0.9434 (pp) REVERT: E 504 LEU cc_start: 0.8586 (mt) cc_final: 0.8318 (mt) REVERT: E 524 ILE cc_start: 0.8092 (mt) cc_final: 0.7695 (mt) REVERT: F 35 VAL cc_start: 0.9107 (m) cc_final: 0.8787 (p) REVERT: F 49 THR cc_start: 0.8965 (m) cc_final: 0.8385 (t) REVERT: F 51 TYR cc_start: 0.6822 (t80) cc_final: 0.6476 (t80) REVERT: F 53 LEU cc_start: 0.9216 (mt) cc_final: 0.8648 (mm) REVERT: F 114 ASN cc_start: 0.8876 (t0) cc_final: 0.8672 (m-40) REVERT: F 411 TYR cc_start: 0.6633 (m-80) cc_final: 0.6063 (m-10) REVERT: F 417 LEU cc_start: 0.9641 (mt) cc_final: 0.9367 (pp) REVERT: F 452 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6314 (pp) REVERT: F 504 LEU cc_start: 0.8779 (mt) cc_final: 0.8514 (mt) REVERT: F 505 LYS cc_start: 0.8532 (tptt) cc_final: 0.8326 (mttt) REVERT: F 524 ILE cc_start: 0.7656 (mt) cc_final: 0.7251 (mt) outliers start: 20 outliers final: 0 residues processed: 491 average time/residue: 0.1553 time to fit residues: 109.6218 Evaluate side-chains 341 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 337 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 236 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 235 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 133 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 182 optimal weight: 20.0000 chunk 184 optimal weight: 6.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 120 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 530 GLN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 ASN E 120 GLN ** E 345 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4762 r_free = 0.4762 target = 0.165387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.154295 restraints weight = 182944.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.155176 restraints weight = 152424.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.156020 restraints weight = 130106.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.156602 restraints weight = 116158.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.157045 restraints weight = 106297.220| |-----------------------------------------------------------------------------| r_work (final): 0.4556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5525 moved from start: 0.8869 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= 0.205 Angle : 0.966 10.286 27396 Z= 0.517 Chirality : 0.056 0.409 3084 Planarity : 0.006 0.066 3570 Dihedral : 8.940 60.597 2730 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 1.23 % Allowed : 13.11 % Favored : 85.66 % Rotamer: Outliers : 0.46 % Allowed : 4.73 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 11.11 % Twisted General : 0.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.05 (0.14), residues: 2448 helix: -0.88 (0.19), residues: 672 sheet: -0.84 (0.26), residues: 294 loop : -4.27 (0.11), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 91 TYR 0.022 0.002 TYR B 566 PHE 0.032 0.002 PHE E 143 TRP 0.012 0.002 TRP B 76 HIS 0.006 0.002 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00432 (20346) covalent geometry : angle 0.96602 (27396) hydrogen bonds : bond 0.05827 ( 600) hydrogen bonds : angle 6.90228 ( 1728) *********************** 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 430 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 420 time to evaluate : 0.476 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: symmetry clash REVERT: A 51 TYR cc_start: 0.6370 (t80) cc_final: 0.6053 (t80) REVERT: A 342 GLN cc_start: 0.8781 (pp30) cc_final: 0.8269 (mp10) REVERT: A 362 MET cc_start: 0.6789 (pmm) cc_final: 0.6269 (pmm) REVERT: A 374 LYS cc_start: 0.8765 (tmmt) cc_final: 0.8161 (mtmt) REVERT: A 504 LEU cc_start: 0.8885 (mt) cc_final: 0.8632 (mt) REVERT: A 524 ILE cc_start: 0.8103 (mt) cc_final: 0.7723 (mt) REVERT: B 51 TYR cc_start: 0.6459 (t80) cc_final: 0.5874 (t80) REVERT: B 52 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7213 (tp30) REVERT: B 53 LEU cc_start: 0.9264 (mm) cc_final: 0.8938 (mm) REVERT: B 362 MET cc_start: 0.8165 (pmm) cc_final: 0.7848 (pmm) REVERT: B 448 ASP cc_start: 0.9342 (t0) cc_final: 0.8614 (p0) REVERT: B 524 ILE cc_start: 0.8288 (mt) cc_final: 0.7925 (mt) REVERT: B 525 ILE cc_start: 0.6304 (mt) cc_final: 0.6039 (mt) REVERT: C 51 TYR cc_start: 0.6413 (t80) cc_final: 0.6098 (t80) REVERT: C 52 GLU cc_start: 0.8346 (pp20) cc_final: 0.7952 (pp20) REVERT: C 90 MET cc_start: 0.7804 (tpp) cc_final: 0.7163 (mmm) REVERT: C 362 MET cc_start: 0.7740 (pmm) cc_final: 0.6862 (pmm) REVERT: C 504 LEU cc_start: 0.8629 (mt) cc_final: 0.8362 (mt) REVERT: C 524 ILE cc_start: 0.8018 (mt) cc_final: 0.7644 (mt) REVERT: D 51 TYR cc_start: 0.6388 (t80) cc_final: 0.6071 (t80) REVERT: D 342 GLN cc_start: 0.8767 (pp30) cc_final: 0.8260 (mp10) REVERT: D 362 MET cc_start: 0.6811 (pmm) cc_final: 0.6315 (pmm) REVERT: D 374 LYS cc_start: 0.8757 (tmmt) cc_final: 0.8153 (mtmt) REVERT: D 461 GLU cc_start: 0.7586 (pp20) cc_final: 0.7359 (pp20) REVERT: D 504 LEU cc_start: 0.8888 (mt) cc_final: 0.8625 (mt) REVERT: D 524 ILE cc_start: 0.8142 (mt) cc_final: 0.7753 (mt) REVERT: E 51 TYR cc_start: 0.6459 (t80) cc_final: 0.5882 (t80) REVERT: E 52 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7208 (tp30) REVERT: E 53 LEU cc_start: 0.9269 (mm) cc_final: 0.8947 (mm) REVERT: E 362 MET cc_start: 0.8140 (pmm) cc_final: 0.7793 (pmm) REVERT: E 448 ASP cc_start: 0.9386 (t0) cc_final: 0.8670 (p0) REVERT: E 524 ILE cc_start: 0.8251 (mt) cc_final: 0.7888 (mt) REVERT: E 525 ILE cc_start: 0.6265 (mt) cc_final: 0.5998 (mt) REVERT: F 51 TYR cc_start: 0.6453 (t80) cc_final: 0.6108 (t80) REVERT: F 52 GLU cc_start: 0.8350 (pp20) cc_final: 0.7950 (pp20) REVERT: F 90 MET cc_start: 0.7821 (tpp) cc_final: 0.7180 (mmm) REVERT: F 362 MET cc_start: 0.7720 (pmm) cc_final: 0.6838 (pmm) REVERT: F 504 LEU cc_start: 0.8640 (mt) cc_final: 0.8370 (mt) REVERT: F 524 ILE cc_start: 0.8002 (mt) cc_final: 0.7627 (mt) outliers start: 10 outliers final: 7 residues processed: 430 average time/residue: 0.1545 time to fit residues: 96.2987 Evaluate side-chains 338 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 331 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 56 optimal weight: 30.0000 chunk 63 optimal weight: 40.0000 chunk 58 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 240 optimal weight: 0.0030 chunk 242 optimal weight: 20.0000 chunk 239 optimal weight: 20.0000 chunk 130 optimal weight: 20.0000 chunk 83 optimal weight: 0.0980 overall best weight: 5.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 GLN A 342 GLN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 ASN ** 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 530 GLN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN D 342 GLN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 530 GLN F 120 GLN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.163026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.152027 restraints weight = 179279.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.152904 restraints weight = 148840.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.153461 restraints weight = 128072.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.154022 restraints weight = 116820.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.154371 restraints weight = 106182.950| |-----------------------------------------------------------------------------| r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5786 moved from start: 1.0137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20346 Z= 0.197 Angle : 0.923 9.401 27396 Z= 0.493 Chirality : 0.057 0.484 3084 Planarity : 0.006 0.052 3570 Dihedral : 8.196 54.102 2730 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 26.99 Ramachandran Plot: Outliers : 1.14 % Allowed : 13.11 % Favored : 85.74 % Rotamer: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.98 (0.14), residues: 2448 helix: -0.79 (0.19), residues: 666 sheet: -1.28 (0.27), residues: 306 loop : -4.13 (0.12), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 560 TYR 0.033 0.002 TYR A 566 PHE 0.025 0.002 PHE A 143 TRP 0.008 0.002 TRP B 320 HIS 0.003 0.001 HIS D 171 Details of bonding type rmsd covalent geometry : bond 0.00402 (20346) covalent geometry : angle 0.92253 (27396) hydrogen bonds : bond 0.05387 ( 600) hydrogen bonds : angle 6.56666 ( 1728) *********************** 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 435 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 433 time to evaluate : 0.955 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: A 51 TYR cc_start: 0.7060 (t80) cc_final: 0.6437 (t80) REVERT: A 342 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8251 (mm-40) REVERT: A 351 PHE cc_start: 0.9103 (m-80) cc_final: 0.8898 (m-80) REVERT: A 362 MET cc_start: 0.5964 (pmm) cc_final: 0.5721 (pmm) REVERT: A 411 TYR cc_start: 0.6414 (m-10) cc_final: 0.6195 (m-10) REVERT: A 497 ASN cc_start: 0.8933 (m110) cc_final: 0.8161 (p0) REVERT: A 504 LEU cc_start: 0.9032 (mt) cc_final: 0.8648 (mt) REVERT: A 524 ILE cc_start: 0.8638 (mt) cc_final: 0.8133 (mt) REVERT: B 51 TYR cc_start: 0.7107 (t80) cc_final: 0.6417 (t80) REVERT: B 52 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7673 (tp30) REVERT: B 53 LEU cc_start: 0.9401 (mm) cc_final: 0.9088 (mm) REVERT: B 61 ARG cc_start: 0.9407 (ttp-110) cc_final: 0.9118 (ptp-110) REVERT: B 114 ASN cc_start: 0.8393 (m-40) cc_final: 0.7909 (m-40) REVERT: B 342 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8420 (mm-40) REVERT: B 504 LEU cc_start: 0.9175 (mt) cc_final: 0.8691 (mt) REVERT: B 524 ILE cc_start: 0.8606 (mt) cc_final: 0.8340 (mt) REVERT: B 525 ILE cc_start: 0.7461 (mt) cc_final: 0.7184 (mm) REVERT: C 51 TYR cc_start: 0.7250 (t80) cc_final: 0.6312 (t80) REVERT: C 76 TRP cc_start: 0.6655 (t60) cc_final: 0.6281 (t60) REVERT: C 86 ARG cc_start: 0.8209 (tpp-160) cc_final: 0.7900 (tpp-160) REVERT: C 90 MET cc_start: 0.7540 (tpp) cc_final: 0.7331 (mmm) REVERT: C 351 PHE cc_start: 0.9071 (m-80) cc_final: 0.8864 (m-80) REVERT: C 504 LEU cc_start: 0.8809 (mt) cc_final: 0.8355 (mt) REVERT: C 524 ILE cc_start: 0.8495 (mt) cc_final: 0.8049 (mt) REVERT: D 51 TYR cc_start: 0.7055 (t80) cc_final: 0.6416 (t80) REVERT: D 56 TYR cc_start: 0.8963 (t80) cc_final: 0.8685 (t80) REVERT: D 60 LYS cc_start: 0.9518 (tttt) cc_final: 0.9239 (tppt) REVERT: D 342 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8234 (mm-40) REVERT: D 351 PHE cc_start: 0.9106 (m-80) cc_final: 0.8899 (m-80) REVERT: D 362 MET cc_start: 0.6038 (pmm) cc_final: 0.5829 (pmm) REVERT: D 411 TYR cc_start: 0.6802 (m-10) cc_final: 0.6433 (m-10) REVERT: D 448 ASP cc_start: 0.9139 (t0) cc_final: 0.8903 (p0) REVERT: D 461 GLU cc_start: 0.7713 (pp20) cc_final: 0.7455 (pp20) REVERT: D 504 LEU cc_start: 0.9069 (mt) cc_final: 0.8690 (mt) REVERT: D 524 ILE cc_start: 0.8634 (mt) cc_final: 0.8128 (mt) REVERT: E 51 TYR cc_start: 0.7091 (t80) cc_final: 0.6399 (t80) REVERT: E 52 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7669 (tp30) REVERT: E 53 LEU cc_start: 0.9395 (mm) cc_final: 0.9081 (mm) REVERT: E 61 ARG cc_start: 0.9404 (ttp-110) cc_final: 0.9117 (ptp-110) REVERT: E 114 ASN cc_start: 0.8390 (m-40) cc_final: 0.7904 (m-40) REVERT: E 342 GLN cc_start: 0.8872 (tm-30) cc_final: 0.8440 (mm-40) REVERT: E 504 LEU cc_start: 0.9161 (mt) cc_final: 0.8674 (mt) REVERT: E 524 ILE cc_start: 0.8575 (mt) cc_final: 0.8319 (mt) REVERT: E 525 ILE cc_start: 0.7452 (mt) cc_final: 0.7175 (mm) REVERT: F 51 TYR cc_start: 0.7240 (t80) cc_final: 0.6300 (t80) REVERT: F 76 TRP cc_start: 0.6640 (t60) cc_final: 0.6264 (t60) REVERT: F 86 ARG cc_start: 0.8198 (tpp-160) cc_final: 0.7891 (tpp-160) REVERT: F 90 MET cc_start: 0.7555 (tpp) cc_final: 0.7337 (mmm) REVERT: F 351 PHE cc_start: 0.9050 (m-80) cc_final: 0.8844 (m-80) REVERT: F 504 LEU cc_start: 0.8813 (mt) cc_final: 0.8362 (mt) REVERT: F 532 TYR cc_start: 0.7883 (t80) cc_final: 0.7561 (t80) outliers start: 2 outliers final: 0 residues processed: 433 average time/residue: 0.1858 time to fit residues: 116.5124 Evaluate side-chains 339 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 337 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 187 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 199 optimal weight: 8.9990 chunk 182 optimal weight: 40.0000 chunk 74 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 222 optimal weight: 0.7980 chunk 198 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- 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 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 GLN ** 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 48 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 GLN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 407 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.160080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.149105 restraints weight = 180215.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.150055 restraints weight = 150354.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.150757 restraints weight = 127340.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.151317 restraints weight = 114891.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.151674 restraints weight = 105219.251| |-----------------------------------------------------------------------------| r_work (final): 0.4444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5826 moved from start: 1.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20346 Z= 0.211 Angle : 0.941 12.342 27396 Z= 0.495 Chirality : 0.058 0.588 3084 Planarity : 0.006 0.052 3570 Dihedral : 8.136 54.612 2730 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 27.90 Ramachandran Plot: Outliers : 0.82 % Allowed : 13.48 % Favored : 85.70 % Rotamer: Outliers : 0.14 % Allowed : 4.55 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.97 (0.14), residues: 2448 helix: -0.91 (0.18), residues: 666 sheet: -1.38 (0.27), residues: 294 loop : -4.01 (0.13), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 61 TYR 0.025 0.002 TYR C 566 PHE 0.038 0.003 PHE A 143 TRP 0.011 0.002 TRP E 320 HIS 0.008 0.002 HIS C 407 Details of bonding type rmsd covalent geometry : bond 0.00426 (20346) covalent geometry : angle 0.94079 (27396) hydrogen bonds : bond 0.05409 ( 600) hydrogen bonds : angle 6.62144 ( 1728) *********************** 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 423 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 420 time to evaluate : 0.831 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: A 51 TYR cc_start: 0.7388 (t80) cc_final: 0.6741 (t80) REVERT: A 342 GLN cc_start: 0.9174 (pp30) cc_final: 0.8180 (mp10) REVERT: A 351 PHE cc_start: 0.9191 (m-80) cc_final: 0.8943 (m-80) REVERT: A 374 LYS cc_start: 0.9037 (tmmt) cc_final: 0.8823 (tmtt) REVERT: A 461 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7984 (mp0) REVERT: A 504 LEU cc_start: 0.9130 (mt) cc_final: 0.8805 (mt) REVERT: A 524 ILE cc_start: 0.8908 (mt) cc_final: 0.8337 (mt) REVERT: A 557 ASN cc_start: 0.7217 (m-40) cc_final: 0.6337 (t0) REVERT: B 51 TYR cc_start: 0.7460 (t80) cc_final: 0.6802 (t80) REVERT: B 53 LEU cc_start: 0.9231 (mm) cc_final: 0.9004 (mm) REVERT: B 61 ARG cc_start: 0.9389 (ttp-110) cc_final: 0.9039 (ptp-110) REVERT: B 114 ASN cc_start: 0.8817 (m-40) cc_final: 0.8237 (m-40) REVERT: B 342 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8547 (mm110) REVERT: B 461 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 504 LEU cc_start: 0.9018 (mt) cc_final: 0.8759 (mt) REVERT: B 524 ILE cc_start: 0.8524 (mt) cc_final: 0.8120 (mt) REVERT: B 525 ILE cc_start: 0.7957 (mt) cc_final: 0.7732 (mm) REVERT: C 35 VAL cc_start: 0.7983 (p) cc_final: 0.7755 (p) REVERT: C 51 TYR cc_start: 0.7060 (t80) cc_final: 0.6699 (t80) REVERT: C 76 TRP cc_start: 0.6727 (t60) cc_final: 0.6458 (t60) REVERT: C 86 ARG cc_start: 0.8021 (tpp-160) cc_final: 0.7696 (tpp80) REVERT: C 351 PHE cc_start: 0.9129 (m-80) cc_final: 0.8925 (m-80) REVERT: C 504 LEU cc_start: 0.8844 (mt) cc_final: 0.8374 (mt) REVERT: C 524 ILE cc_start: 0.8836 (mt) cc_final: 0.8546 (mt) REVERT: D 51 TYR cc_start: 0.7464 (t80) cc_final: 0.6829 (t80) REVERT: D 342 GLN cc_start: 0.9169 (pp30) cc_final: 0.8158 (mp10) REVERT: D 351 PHE cc_start: 0.9194 (m-80) cc_final: 0.8940 (m-80) REVERT: D 461 GLU cc_start: 0.7765 (pp20) cc_final: 0.7535 (pp20) REVERT: D 497 ASN cc_start: 0.9534 (m-40) cc_final: 0.8753 (p0) REVERT: D 504 LEU cc_start: 0.9130 (mt) cc_final: 0.8799 (mt) REVERT: D 524 ILE cc_start: 0.8915 (mt) cc_final: 0.8355 (mt) REVERT: D 557 ASN cc_start: 0.7203 (m-40) cc_final: 0.6333 (t0) REVERT: E 51 TYR cc_start: 0.7457 (t80) cc_final: 0.6802 (t80) REVERT: E 53 LEU cc_start: 0.9235 (mm) cc_final: 0.9013 (mm) REVERT: E 61 ARG cc_start: 0.9392 (ttp-110) cc_final: 0.9044 (ptp-110) REVERT: E 114 ASN cc_start: 0.8865 (m-40) cc_final: 0.8295 (m-40) REVERT: E 342 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8547 (mm110) REVERT: E 461 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8159 (tm-30) REVERT: E 504 LEU cc_start: 0.9023 (mt) cc_final: 0.8762 (mt) REVERT: E 524 ILE cc_start: 0.8528 (mt) cc_final: 0.8133 (mt) REVERT: E 525 ILE cc_start: 0.7968 (mt) cc_final: 0.7742 (mm) REVERT: F 35 VAL cc_start: 0.8002 (p) cc_final: 0.7775 (p) REVERT: F 51 TYR cc_start: 0.7054 (t80) cc_final: 0.6692 (t80) REVERT: F 76 TRP cc_start: 0.6745 (t60) cc_final: 0.6480 (t60) REVERT: F 86 ARG cc_start: 0.7997 (tpp-160) cc_final: 0.7676 (tpp80) REVERT: F 504 LEU cc_start: 0.8857 (mt) cc_final: 0.8281 (mt) REVERT: F 524 ILE cc_start: 0.8403 (mp) cc_final: 0.7928 (mp) outliers start: 3 outliers final: 1 residues processed: 423 average time/residue: 0.1860 time to fit residues: 114.2997 Evaluate side-chains 331 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 220 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 224 optimal weight: 0.4980 chunk 43 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 152 optimal weight: 6.9990 chunk 215 optimal weight: 50.0000 chunk 108 optimal weight: 7.9990 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 279 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 279 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 ASN ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** 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 = 0.4729 r_free = 0.4729 target = 0.163682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.152735 restraints weight = 177874.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.153641 restraints weight = 148020.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.154418 restraints weight = 125802.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4668 r_free = 0.4668 target = 0.155048 restraints weight = 112733.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.155441 restraints weight = 102889.613| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5664 moved from start: 1.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20346 Z= 0.162 Angle : 0.866 9.974 27396 Z= 0.458 Chirality : 0.054 0.513 3084 Planarity : 0.005 0.056 3570 Dihedral : 7.553 53.248 2730 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.82 % Allowed : 13.28 % Favored : 85.91 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.15), residues: 2448 helix: -0.69 (0.19), residues: 684 sheet: -1.89 (0.24), residues: 336 loop : -3.87 (0.13), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 61 TYR 0.022 0.002 TYR F 532 PHE 0.031 0.002 PHE D 143 TRP 0.006 0.001 TRP B 320 HIS 0.003 0.001 HIS A 345 Details of bonding type rmsd covalent geometry : bond 0.00336 (20346) covalent geometry : angle 0.86556 (27396) hydrogen bonds : bond 0.05062 ( 600) hydrogen bonds : angle 6.08538 ( 1728) *********************** 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: 0 poor density : 408 time to evaluate : 0.770 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: A 51 TYR cc_start: 0.7558 (t80) cc_final: 0.6898 (t80) REVERT: A 60 LYS cc_start: 0.9460 (tttt) cc_final: 0.9246 (tppt) REVERT: A 342 GLN cc_start: 0.9139 (pp30) cc_final: 0.8271 (mm-40) REVERT: A 504 LEU cc_start: 0.8876 (mt) cc_final: 0.8527 (mt) REVERT: A 524 ILE cc_start: 0.8793 (mt) cc_final: 0.8133 (mt) REVERT: A 557 ASN cc_start: 0.7223 (m-40) cc_final: 0.6256 (t0) REVERT: B 51 TYR cc_start: 0.7305 (t80) cc_final: 0.6667 (t80) REVERT: B 53 LEU cc_start: 0.9275 (mm) cc_final: 0.9040 (mm) REVERT: B 55 ASN cc_start: 0.9402 (m110) cc_final: 0.9172 (m110) REVERT: B 61 ARG cc_start: 0.9332 (ttp-110) cc_final: 0.8923 (ptp-110) REVERT: B 114 ASN cc_start: 0.8330 (m-40) cc_final: 0.7840 (m-40) REVERT: B 342 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8561 (mm-40) REVERT: B 380 ARG cc_start: 0.8924 (tmm160) cc_final: 0.8633 (tmm160) REVERT: B 394 ASN cc_start: 0.6525 (t0) cc_final: 0.5992 (t0) REVERT: B 461 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7658 (tm-30) REVERT: B 504 LEU cc_start: 0.8907 (mt) cc_final: 0.8592 (mt) REVERT: B 524 ILE cc_start: 0.8293 (mt) cc_final: 0.7872 (mt) REVERT: C 35 VAL cc_start: 0.8108 (p) cc_final: 0.7823 (p) REVERT: C 51 TYR cc_start: 0.7038 (t80) cc_final: 0.6821 (t80) REVERT: C 86 ARG cc_start: 0.8543 (tpp-160) cc_final: 0.8231 (tpp-160) REVERT: C 394 ASN cc_start: 0.7205 (m110) cc_final: 0.6864 (m110) REVERT: C 504 LEU cc_start: 0.8753 (mt) cc_final: 0.8352 (mt) REVERT: C 524 ILE cc_start: 0.8692 (mt) cc_final: 0.8152 (mt) REVERT: C 525 ILE cc_start: 0.7631 (mt) cc_final: 0.7425 (mt) REVERT: D 51 TYR cc_start: 0.7490 (t80) cc_final: 0.6901 (t80) REVERT: D 342 GLN cc_start: 0.9099 (pp30) cc_final: 0.8263 (mm-40) REVERT: D 351 PHE cc_start: 0.9002 (m-80) cc_final: 0.8799 (m-80) REVERT: D 461 GLU cc_start: 0.7785 (pp20) cc_final: 0.7408 (pp20) REVERT: D 504 LEU cc_start: 0.8889 (mt) cc_final: 0.8530 (mt) REVERT: D 524 ILE cc_start: 0.8804 (mt) cc_final: 0.8166 (mt) REVERT: D 557 ASN cc_start: 0.7263 (m-40) cc_final: 0.6283 (t0) REVERT: E 51 TYR cc_start: 0.7274 (t80) cc_final: 0.6637 (t80) REVERT: E 53 LEU cc_start: 0.9266 (mm) cc_final: 0.9031 (mm) REVERT: E 55 ASN cc_start: 0.9409 (m110) cc_final: 0.9180 (m110) REVERT: E 61 ARG cc_start: 0.9315 (ttp-110) cc_final: 0.8907 (ptp-110) REVERT: E 114 ASN cc_start: 0.8329 (m-40) cc_final: 0.7837 (m-40) REVERT: E 342 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8547 (mm-40) REVERT: E 380 ARG cc_start: 0.8929 (tmm160) cc_final: 0.8628 (tmm160) REVERT: E 394 ASN cc_start: 0.6476 (t0) cc_final: 0.5940 (t0) REVERT: E 461 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7684 (tm-30) REVERT: E 504 LEU cc_start: 0.8994 (mt) cc_final: 0.8770 (mt) REVERT: E 524 ILE cc_start: 0.8311 (mt) cc_final: 0.7879 (mt) REVERT: F 35 VAL cc_start: 0.8144 (p) cc_final: 0.7856 (p) REVERT: F 51 TYR cc_start: 0.7024 (t80) cc_final: 0.6806 (t80) REVERT: F 86 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8230 (tpp-160) REVERT: F 394 ASN cc_start: 0.7196 (m110) cc_final: 0.6844 (m110) REVERT: F 504 LEU cc_start: 0.8715 (mt) cc_final: 0.8305 (mt) REVERT: F 524 ILE cc_start: 0.8291 (mp) cc_final: 0.7634 (mp) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1847 time to fit residues: 108.3426 Evaluate side-chains 318 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 133 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 155 optimal weight: 40.0000 chunk 215 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 52 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 72 optimal weight: 0.0370 chunk 7 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 chunk 61 optimal weight: 20.0000 overall best weight: 10.0068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 ASN A 144 ASN A 279 ASN B 279 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 ASN C 144 ASN ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN D 279 ASN E 48 ASN E 279 ASN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 406 ASN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 453 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.152606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.141822 restraints weight = 183566.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.142718 restraints weight = 151833.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.143619 restraints weight = 128675.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.144201 restraints weight = 113596.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.144619 restraints weight = 102244.534| |-----------------------------------------------------------------------------| r_work (final): 0.4406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 1.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 20346 Z= 0.282 Angle : 1.053 10.437 27396 Z= 0.557 Chirality : 0.059 0.403 3084 Planarity : 0.007 0.061 3570 Dihedral : 8.539 50.063 2730 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 36.10 Ramachandran Plot: Outliers : 1.10 % Allowed : 16.75 % Favored : 82.15 % Rotamer: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.35 (0.14), residues: 2448 helix: -1.41 (0.17), residues: 678 sheet: -2.12 (0.25), residues: 330 loop : -4.07 (0.13), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 180 TYR 0.035 0.003 TYR E 566 PHE 0.040 0.003 PHE B 143 TRP 0.015 0.003 TRP B 320 HIS 0.006 0.003 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00597 (20346) covalent geometry : angle 1.05339 (27396) hydrogen bonds : bond 0.05859 ( 600) hydrogen bonds : angle 7.16230 ( 1728) *********************** 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 401 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 0.834 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: 0.7831 (t80) cc_final: 0.7379 (t80) REVERT: A 55 ASN cc_start: 0.9491 (m-40) cc_final: 0.9250 (m-40) REVERT: A 342 GLN cc_start: 0.9207 (pp30) cc_final: 0.8482 (mp10) REVERT: A 351 PHE cc_start: 0.9061 (m-80) cc_final: 0.8804 (m-80) REVERT: A 461 GLU cc_start: 0.8579 (tm-30) cc_final: 0.7975 (tm-30) REVERT: A 504 LEU cc_start: 0.9135 (mt) cc_final: 0.8881 (mt) REVERT: A 524 ILE cc_start: 0.9163 (mt) cc_final: 0.8626 (mt) REVERT: A 532 TYR cc_start: 0.7800 (t80) cc_final: 0.7382 (t80) REVERT: B 51 TYR cc_start: 0.7524 (t80) cc_final: 0.6866 (t80) REVERT: B 53 LEU cc_start: 0.9378 (mm) cc_final: 0.9175 (mm) REVERT: B 55 ASN cc_start: 0.9432 (m110) cc_final: 0.9140 (m110) REVERT: B 376 GLN cc_start: 0.9037 (pp30) cc_final: 0.8803 (pp30) REVERT: B 377 LEU cc_start: 0.9196 (mt) cc_final: 0.8539 (mt) REVERT: B 380 ARG cc_start: 0.8802 (tmm160) cc_final: 0.8571 (tmm160) REVERT: B 401 ASP cc_start: 0.8266 (t70) cc_final: 0.7563 (p0) REVERT: B 461 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7922 (tm-30) REVERT: B 499 PHE cc_start: 0.8705 (m-10) cc_final: 0.8474 (m-80) REVERT: B 504 LEU cc_start: 0.9067 (mt) cc_final: 0.8783 (mt) REVERT: C 51 TYR cc_start: 0.7275 (t80) cc_final: 0.6934 (t80) REVERT: C 60 LYS cc_start: 0.9361 (mmpt) cc_final: 0.9119 (mmmt) REVERT: C 86 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7910 (tpp80) REVERT: C 504 LEU cc_start: 0.9124 (mt) cc_final: 0.8739 (mt) REVERT: C 524 ILE cc_start: 0.8938 (mt) cc_final: 0.8448 (mt) REVERT: C 525 ILE cc_start: 0.8680 (mt) cc_final: 0.8050 (mm) REVERT: D 51 TYR cc_start: 0.7722 (t80) cc_final: 0.7309 (t80) REVERT: D 55 ASN cc_start: 0.9484 (m-40) cc_final: 0.9237 (m-40) REVERT: D 342 GLN cc_start: 0.9091 (pp30) cc_final: 0.8454 (mp10) REVERT: D 351 PHE cc_start: 0.9192 (m-80) cc_final: 0.8933 (m-80) REVERT: D 461 GLU cc_start: 0.7931 (pp20) cc_final: 0.7549 (pp20) REVERT: D 504 LEU cc_start: 0.9087 (mt) cc_final: 0.8782 (mt) REVERT: D 524 ILE cc_start: 0.9149 (mt) cc_final: 0.8719 (mt) REVERT: E 51 TYR cc_start: 0.7527 (t80) cc_final: 0.6867 (t80) REVERT: E 53 LEU cc_start: 0.9380 (mm) cc_final: 0.9179 (mm) REVERT: E 55 ASN cc_start: 0.9435 (m110) cc_final: 0.9142 (m110) REVERT: E 376 GLN cc_start: 0.9060 (pp30) cc_final: 0.8837 (pp30) REVERT: E 377 LEU cc_start: 0.9182 (mt) cc_final: 0.8521 (mt) REVERT: E 380 ARG cc_start: 0.8786 (tmm160) cc_final: 0.8472 (tmm160) REVERT: E 394 ASN cc_start: 0.7161 (t0) cc_final: 0.6961 (t0) REVERT: E 401 ASP cc_start: 0.8269 (t70) cc_final: 0.7570 (p0) REVERT: E 461 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7980 (tm-30) REVERT: E 499 PHE cc_start: 0.8663 (m-10) cc_final: 0.8450 (m-80) REVERT: E 504 LEU cc_start: 0.9058 (mt) cc_final: 0.8778 (mt) REVERT: F 51 TYR cc_start: 0.7283 (t80) cc_final: 0.6940 (t80) REVERT: F 60 LYS cc_start: 0.9359 (mmpt) cc_final: 0.9117 (mmmt) REVERT: F 86 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.7792 (tpp80) REVERT: F 351 PHE cc_start: 0.8962 (m-80) cc_final: 0.8731 (m-80) REVERT: F 504 LEU cc_start: 0.9052 (mt) cc_final: 0.8647 (mt) REVERT: F 524 ILE cc_start: 0.8664 (mp) cc_final: 0.7946 (mt) REVERT: F 525 ILE cc_start: 0.8547 (mt) cc_final: 0.7866 (mm) outliers start: 1 outliers final: 0 residues processed: 401 average time/residue: 0.1756 time to fit residues: 101.9357 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 : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 123 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 180 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 103 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 69 optimal weight: 9.9990 chunk 221 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 58 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** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 453 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.156089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.145302 restraints weight = 182779.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.146337 restraints weight = 151125.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.147221 restraints weight = 125252.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.147721 restraints weight = 110368.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.148206 restraints weight = 100015.851| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5868 moved from start: 1.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20346 Z= 0.192 Angle : 0.915 9.641 27396 Z= 0.482 Chirality : 0.055 0.462 3084 Planarity : 0.006 0.066 3570 Dihedral : 7.887 49.861 2730 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.98 % Allowed : 15.11 % Favored : 83.91 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.23 (0.14), residues: 2448 helix: -1.40 (0.18), residues: 708 sheet: -1.97 (0.26), residues: 336 loop : -4.02 (0.13), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 535 TYR 0.033 0.002 TYR D 532 PHE 0.051 0.002 PHE E 143 TRP 0.065 0.003 TRP A 76 HIS 0.004 0.001 HIS E 345 Details of bonding type rmsd covalent geometry : bond 0.00413 (20346) covalent geometry : angle 0.91498 (27396) hydrogen bonds : bond 0.05405 ( 600) hydrogen bonds : angle 6.55563 ( 1728) *********************** 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 397 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.870 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: A 51 TYR cc_start: 0.7739 (t80) cc_final: 0.7354 (t80) REVERT: A 55 ASN cc_start: 0.9508 (m-40) cc_final: 0.9261 (m-40) REVERT: A 342 GLN cc_start: 0.9199 (pp30) cc_final: 0.8482 (mm-40) REVERT: A 449 LEU cc_start: 0.8655 (mp) cc_final: 0.8059 (mp) REVERT: A 461 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8243 (mp0) REVERT: A 504 LEU cc_start: 0.8929 (mt) cc_final: 0.8531 (mt) REVERT: A 525 ILE cc_start: 0.8713 (mt) cc_final: 0.8426 (mm) REVERT: B 51 TYR cc_start: 0.7520 (t80) cc_final: 0.6892 (t80) REVERT: B 342 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8678 (mm-40) REVERT: B 461 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 499 PHE cc_start: 0.8632 (m-10) cc_final: 0.8414 (m-80) REVERT: B 504 LEU cc_start: 0.9008 (mt) cc_final: 0.8801 (mt) REVERT: C 51 TYR cc_start: 0.7283 (t80) cc_final: 0.7074 (t80) REVERT: C 52 GLU cc_start: 0.8750 (pp20) cc_final: 0.8502 (pp20) REVERT: C 55 ASN cc_start: 0.9113 (m-40) cc_final: 0.8873 (m-40) REVERT: C 342 GLN cc_start: 0.9202 (pp30) cc_final: 0.8686 (mm-40) REVERT: C 504 LEU cc_start: 0.8832 (mt) cc_final: 0.8484 (mt) REVERT: C 524 ILE cc_start: 0.8841 (mt) cc_final: 0.8224 (mt) REVERT: C 525 ILE cc_start: 0.8697 (mt) cc_final: 0.8018 (mm) REVERT: D 51 TYR cc_start: 0.7675 (t80) cc_final: 0.7301 (t80) REVERT: D 55 ASN cc_start: 0.9474 (m-40) cc_final: 0.9223 (m-40) REVERT: D 90 MET cc_start: 0.8164 (mmm) cc_final: 0.7956 (mmm) REVERT: D 342 GLN cc_start: 0.9200 (pp30) cc_final: 0.8699 (mp10) REVERT: D 351 PHE cc_start: 0.9204 (m-80) cc_final: 0.8948 (m-80) REVERT: D 461 GLU cc_start: 0.8026 (pp20) cc_final: 0.7693 (pp20) REVERT: D 504 LEU cc_start: 0.8838 (mt) cc_final: 0.8539 (mt) REVERT: D 524 ILE cc_start: 0.9101 (mt) cc_final: 0.8582 (mt) REVERT: D 525 ILE cc_start: 0.8646 (mt) cc_final: 0.7854 (mm) REVERT: E 51 TYR cc_start: 0.7507 (t80) cc_final: 0.6880 (t80) REVERT: E 342 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8690 (mm-40) REVERT: E 461 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8222 (tm-30) REVERT: E 499 PHE cc_start: 0.8641 (m-10) cc_final: 0.8333 (m-80) REVERT: E 504 LEU cc_start: 0.9015 (mt) cc_final: 0.8812 (mt) REVERT: F 51 TYR cc_start: 0.7300 (t80) cc_final: 0.7081 (t80) REVERT: F 52 GLU cc_start: 0.8742 (pp20) cc_final: 0.8492 (pp20) REVERT: F 55 ASN cc_start: 0.9098 (m-40) cc_final: 0.8856 (m-40) REVERT: F 342 GLN cc_start: 0.9134 (pp30) cc_final: 0.8639 (mm-40) REVERT: F 351 PHE cc_start: 0.8885 (m-80) cc_final: 0.8603 (m-80) REVERT: F 504 LEU cc_start: 0.8816 (mt) cc_final: 0.8407 (mt) REVERT: F 524 ILE cc_start: 0.8350 (mp) cc_final: 0.7652 (mp) REVERT: F 525 ILE cc_start: 0.8720 (mt) cc_final: 0.8170 (mm) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1730 time to fit residues: 100.0608 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 : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 210 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 184 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 376 GLN D 144 ASN E 58 GLN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.153413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.142343 restraints weight = 180306.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.143242 restraints weight = 152929.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.144009 restraints weight = 130900.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.144657 restraints weight = 117447.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.145002 restraints weight = 106635.420| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 1.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 20346 Z= 0.220 Angle : 0.959 8.790 27396 Z= 0.509 Chirality : 0.056 0.367 3084 Planarity : 0.006 0.054 3570 Dihedral : 8.108 46.298 2730 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 31.04 Ramachandran Plot: Outliers : 1.06 % Allowed : 17.08 % Favored : 81.86 % Rotamer: Outliers : 0.05 % Allowed : 1.42 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.61 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.14), residues: 2448 helix: -1.46 (0.17), residues: 690 sheet: -2.18 (0.26), residues: 330 loop : -4.03 (0.13), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 535 TYR 0.038 0.003 TYR C 566 PHE 0.039 0.003 PHE B 143 TRP 0.056 0.003 TRP A 76 HIS 0.007 0.002 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00470 (20346) covalent geometry : angle 0.95918 (27396) hydrogen bonds : bond 0.05586 ( 600) hydrogen bonds : angle 6.92652 ( 1728) *********************** 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 393 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 392 time to evaluate : 0.791 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: A 51 TYR cc_start: 0.7705 (t80) cc_final: 0.7266 (t80) REVERT: A 55 ASN cc_start: 0.9437 (m-40) cc_final: 0.9146 (m-40) REVERT: A 342 GLN cc_start: 0.9255 (pp30) cc_final: 0.8673 (mp10) REVERT: A 351 PHE cc_start: 0.9242 (m-80) cc_final: 0.8927 (m-80) REVERT: A 461 GLU cc_start: 0.8610 (tm-30) cc_final: 0.7697 (tm-30) REVERT: A 504 LEU cc_start: 0.8558 (mt) cc_final: 0.8266 (mt) REVERT: A 535 ARG cc_start: 0.8776 (pmt-80) cc_final: 0.8416 (pmt-80) REVERT: B 51 TYR cc_start: 0.7626 (t80) cc_final: 0.6952 (t80) REVERT: B 55 ASN cc_start: 0.9275 (m110) cc_final: 0.9053 (m110) REVERT: B 342 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8728 (mm-40) REVERT: B 461 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 497 ASN cc_start: 0.9516 (m-40) cc_final: 0.8753 (m-40) REVERT: B 499 PHE cc_start: 0.8670 (m-10) cc_final: 0.8416 (m-80) REVERT: C 51 TYR cc_start: 0.7118 (t80) cc_final: 0.6910 (t80) REVERT: C 52 GLU cc_start: 0.8618 (pp20) cc_final: 0.8379 (pp20) REVERT: C 342 GLN cc_start: 0.9204 (pp30) cc_final: 0.8312 (mm110) REVERT: C 449 LEU cc_start: 0.9058 (mp) cc_final: 0.8596 (mp) REVERT: C 504 LEU cc_start: 0.8763 (mt) cc_final: 0.8386 (mt) REVERT: C 567 PRO cc_start: 0.8419 (Cg_exo) cc_final: 0.8207 (Cg_endo) REVERT: D 51 TYR cc_start: 0.7718 (t80) cc_final: 0.7301 (t80) REVERT: D 55 ASN cc_start: 0.9441 (m-40) cc_final: 0.9170 (m-40) REVERT: D 56 TYR cc_start: 0.9392 (t80) cc_final: 0.8464 (t80) REVERT: D 90 MET cc_start: 0.7962 (mmm) cc_final: 0.7654 (mmm) REVERT: D 342 GLN cc_start: 0.9252 (pp30) cc_final: 0.8745 (mp10) REVERT: D 351 PHE cc_start: 0.9289 (m-80) cc_final: 0.9028 (m-80) REVERT: D 461 GLU cc_start: 0.8137 (pp20) cc_final: 0.7762 (pp20) REVERT: D 504 LEU cc_start: 0.8805 (mt) cc_final: 0.8507 (mt) REVERT: D 524 ILE cc_start: 0.9160 (mt) cc_final: 0.8527 (mt) REVERT: D 525 ILE cc_start: 0.8646 (mt) cc_final: 0.7842 (mm) REVERT: E 51 TYR cc_start: 0.7654 (t80) cc_final: 0.6975 (t80) REVERT: E 55 ASN cc_start: 0.9285 (m110) cc_final: 0.9060 (m110) REVERT: E 342 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8743 (mm-40) REVERT: E 401 ASP cc_start: 0.8373 (t70) cc_final: 0.7586 (p0) REVERT: E 461 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7954 (tm-30) REVERT: E 499 PHE cc_start: 0.8674 (m-10) cc_final: 0.8374 (m-80) REVERT: F 51 TYR cc_start: 0.7178 (t80) cc_final: 0.6962 (t80) REVERT: F 52 GLU cc_start: 0.8570 (pp20) cc_final: 0.8306 (pp20) REVERT: F 342 GLN cc_start: 0.9198 (pp30) cc_final: 0.8242 (mp10) REVERT: F 504 LEU cc_start: 0.8762 (mt) cc_final: 0.8348 (mt) outliers start: 1 outliers final: 0 residues processed: 393 average time/residue: 0.1781 time to fit residues: 101.2671 Evaluate side-chains 333 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 247 optimal weight: 5.9990 chunk 144 optimal weight: 40.0000 chunk 1 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 62 optimal weight: 40.0000 chunk 229 optimal weight: 0.7980 chunk 215 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 135 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 overall best weight: 7.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 144 ASN ** F 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 530 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.152400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.141289 restraints weight = 181764.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.142039 restraints weight = 152723.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.142965 restraints weight = 131455.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.143656 restraints weight = 115226.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.143903 restraints weight = 105494.738| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 1.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20346 Z= 0.216 Angle : 0.980 13.111 27396 Z= 0.519 Chirality : 0.055 0.304 3084 Planarity : 0.006 0.069 3570 Dihedral : 8.043 50.659 2730 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 31.22 Ramachandran Plot: Outliers : 1.14 % Allowed : 16.67 % Favored : 82.19 % Rotamer: Outliers : 0.05 % Allowed : 1.06 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.22 (0.14), residues: 2448 helix: -1.45 (0.18), residues: 690 sheet: -2.20 (0.26), residues: 330 loop : -3.88 (0.13), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 91 TYR 0.035 0.003 TYR A 532 PHE 0.034 0.003 PHE A 143 TRP 0.050 0.003 TRP A 76 HIS 0.005 0.002 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00454 (20346) covalent geometry : angle 0.97978 (27396) hydrogen bonds : bond 0.05597 ( 600) hydrogen bonds : angle 7.01978 ( 1728) ********************** 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 401 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 0.791 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: A 51 TYR cc_start: 0.7707 (t80) cc_final: 0.7274 (t80) REVERT: A 55 ASN cc_start: 0.9434 (m-40) cc_final: 0.9041 (m-40) REVERT: A 56 TYR cc_start: 0.9341 (t80) cc_final: 0.9113 (t80) REVERT: A 60 LYS cc_start: 0.9595 (tttt) cc_final: 0.9366 (tppt) REVERT: A 342 GLN cc_start: 0.9271 (pp30) cc_final: 0.8759 (mp10) REVERT: A 351 PHE cc_start: 0.9167 (m-80) cc_final: 0.8956 (m-80) REVERT: A 497 ASN cc_start: 0.9059 (m-40) cc_final: 0.8501 (m-40) REVERT: A 504 LEU cc_start: 0.8727 (mt) cc_final: 0.8423 (mt) REVERT: A 535 ARG cc_start: 0.8841 (pmt-80) cc_final: 0.8610 (pmt-80) REVERT: B 51 TYR cc_start: 0.7656 (t80) cc_final: 0.6992 (t80) REVERT: B 55 ASN cc_start: 0.9281 (m110) cc_final: 0.9065 (m110) REVERT: B 342 GLN cc_start: 0.9153 (tm-30) cc_final: 0.8924 (mm-40) REVERT: B 376 GLN cc_start: 0.9172 (pp30) cc_final: 0.8965 (pp30) REVERT: B 401 ASP cc_start: 0.8284 (t70) cc_final: 0.7308 (p0) REVERT: B 461 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 497 ASN cc_start: 0.9524 (m-40) cc_final: 0.8836 (m-40) REVERT: C 52 GLU cc_start: 0.8630 (pp20) cc_final: 0.8429 (pp20) REVERT: C 342 GLN cc_start: 0.9220 (pp30) cc_final: 0.8301 (mp10) REVERT: C 504 LEU cc_start: 0.8642 (mt) cc_final: 0.8283 (mt) REVERT: C 563 MET cc_start: 0.8176 (mmm) cc_final: 0.7946 (mmm) REVERT: D 51 TYR cc_start: 0.7783 (t80) cc_final: 0.7323 (t80) REVERT: D 55 ASN cc_start: 0.9421 (m-40) cc_final: 0.9107 (m-40) REVERT: D 90 MET cc_start: 0.7959 (mmm) cc_final: 0.7587 (mmm) REVERT: D 342 GLN cc_start: 0.9434 (pp30) cc_final: 0.8884 (mp10) REVERT: D 351 PHE cc_start: 0.9184 (m-80) cc_final: 0.8964 (m-80) REVERT: D 497 ASN cc_start: 0.9268 (m-40) cc_final: 0.8767 (m-40) REVERT: D 504 LEU cc_start: 0.8927 (mt) cc_final: 0.8670 (mt) REVERT: D 535 ARG cc_start: 0.8946 (pmt-80) cc_final: 0.8631 (pmt-80) REVERT: E 51 TYR cc_start: 0.7684 (t80) cc_final: 0.7009 (t80) REVERT: E 55 ASN cc_start: 0.9303 (m110) cc_final: 0.9086 (m110) REVERT: E 342 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8940 (mm-40) REVERT: E 376 GLN cc_start: 0.9163 (pp30) cc_final: 0.8953 (pp30) REVERT: E 401 ASP cc_start: 0.8259 (t70) cc_final: 0.7289 (p0) REVERT: E 461 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8059 (tm-30) REVERT: E 497 ASN cc_start: 0.9521 (m-40) cc_final: 0.8886 (m-40) REVERT: F 41 GLN cc_start: 0.9113 (tt0) cc_final: 0.8905 (tp-100) REVERT: F 52 GLU cc_start: 0.8575 (pp20) cc_final: 0.8368 (pp20) REVERT: F 55 ASN cc_start: 0.9090 (m-40) cc_final: 0.8884 (m-40) REVERT: F 342 GLN cc_start: 0.9170 (pp30) cc_final: 0.8869 (pm20) REVERT: F 449 LEU cc_start: 0.8999 (mp) cc_final: 0.8486 (mp) REVERT: F 504 LEU cc_start: 0.8680 (mt) cc_final: 0.8255 (mt) outliers start: 1 outliers final: 0 residues processed: 401 average time/residue: 0.1770 time to fit residues: 102.7383 Evaluate side-chains 318 residues out of total 2178 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 89 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 233 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 15 optimal weight: 30.0000 chunk 210 optimal weight: 30.0000 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** A 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN C 144 ASN C 279 ASN C 376 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 ASN ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 453 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 144 ASN F 279 ASN ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 376 GLN ** F 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.153218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.142132 restraints weight = 181002.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.143047 restraints weight = 151243.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.144011 restraints weight = 128741.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.144498 restraints weight = 113798.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.144977 restraints weight = 104085.324| |-----------------------------------------------------------------------------| r_work (final): 0.4363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 1.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20346 Z= 0.190 Angle : 0.946 13.143 27396 Z= 0.501 Chirality : 0.055 0.299 3084 Planarity : 0.006 0.075 3570 Dihedral : 7.822 45.543 2730 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 28.03 Ramachandran Plot: Outliers : 0.98 % Allowed : 16.83 % Favored : 82.19 % Rotamer: Outliers : 0.09 % Allowed : 0.87 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.72 % Twisted Proline : 0.00 % Twisted General : 0.41 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.04 (0.15), residues: 2448 helix: -1.28 (0.18), residues: 684 sheet: -2.09 (0.28), residues: 300 loop : -3.74 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 61 TYR 0.025 0.002 TYR A 532 PHE 0.030 0.002 PHE A 143 TRP 0.049 0.002 TRP A 76 HIS 0.004 0.001 HIS B 171 Details of bonding type rmsd covalent geometry : bond 0.00406 (20346) covalent geometry : angle 0.94615 (27396) hydrogen bonds : bond 0.05242 ( 600) hydrogen bonds : angle 6.78937 ( 1728) =============================================================================== Job complete usr+sys time: 3646.62 seconds wall clock time: 64 minutes 4.75 seconds (3844.75 seconds total)