Starting phenix.real_space_refine on Fri Jun 5 13:55:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9urj_64459/06_2026/9urj_64459_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9urj_64459/06_2026/9urj_64459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9urj_64459/06_2026/9urj_64459_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9urj_64459/06_2026/9urj_64459_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9urj_64459/06_2026/9urj_64459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9urj_64459/06_2026/9urj_64459.map" } resolution = 3.11 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 52 5.16 5 C 13244 2.51 5 N 3640 2.21 5 O 3724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20676 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5152 Classifications: {'peptide': 624} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 596} Chain breaks: 6 Chain: "B" Number of atoms: 5152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5152 Classifications: {'peptide': 624} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 596} Chain breaks: 6 Chain: "C" Number of atoms: 5152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5152 Classifications: {'peptide': 624} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 596} Chain breaks: 6 Chain: "D" Number of atoms: 5152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5152 Classifications: {'peptide': 624} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 596} Chain breaks: 6 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'7TT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'7TT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'7TT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'7TT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.41, per 1000 atoms: 0.21 Number of scatterers: 20676 At special positions: 0 Unit cell: (141.913, 127.053, 104.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 16 15.00 O 3724 8.00 N 3640 7.00 C 13244 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: 1.43 Conformation dependent library (CDL) restraints added in 694.0 milliseconds 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 20 sheets defined 43.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 9 through 26 Processing helix chain 'A' and resid 31 through 53 removed outlier: 3.782A pdb=" N GLY A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.580A pdb=" N LEU A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 105 Processing helix chain 'A' and resid 116 through 130 Processing helix chain 'A' and resid 145 through 150 removed outlier: 4.526A pdb=" N PHE A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.804A pdb=" N PHE A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 296 through 303 removed outlier: 3.633A pdb=" N ILE A 301 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.867A pdb=" N ALA A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 removed outlier: 3.850A pdb=" N PHE A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 393 Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 477 through 493 removed outlier: 3.950A pdb=" N GLU A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 527 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 614 through 620 Processing helix chain 'A' and resid 630 through 646 Processing helix chain 'A' and resid 672 through 685 Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 31 through 53 removed outlier: 3.782A pdb=" N GLY B 40 " --> pdb=" O MET B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 64 removed outlier: 3.580A pdb=" N LEU B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 105 Processing helix chain 'B' and resid 116 through 130 Processing helix chain 'B' and resid 145 through 150 removed outlier: 4.526A pdb=" N PHE B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 Processing helix chain 'B' and resid 207 through 212 removed outlier: 3.804A pdb=" N PHE B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 280 Processing helix chain 'B' and resid 296 through 303 removed outlier: 3.633A pdb=" N ILE B 301 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.867A pdb=" N ALA B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 removed outlier: 3.850A pdb=" N PHE B 362 " --> pdb=" O ARG B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 393 Processing helix chain 'B' and resid 415 through 422 Processing helix chain 'B' and resid 477 through 493 removed outlier: 3.950A pdb=" N GLU B 483 " --> pdb=" O ARG B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 527 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 614 through 620 Processing helix chain 'B' and resid 630 through 646 Processing helix chain 'B' and resid 672 through 685 Processing helix chain 'C' and resid 9 through 26 Processing helix chain 'C' and resid 31 through 53 removed outlier: 3.782A pdb=" N GLY C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.580A pdb=" N LEU C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 105 Processing helix chain 'C' and resid 116 through 130 Processing helix chain 'C' and resid 145 through 150 removed outlier: 4.526A pdb=" N PHE C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.804A pdb=" N PHE C 211 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 280 Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.633A pdb=" N ILE C 301 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 339 removed outlier: 3.867A pdb=" N ALA C 335 " --> pdb=" O ASN C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 363 removed outlier: 3.850A pdb=" N PHE C 362 " --> pdb=" O ARG C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 393 Processing helix chain 'C' and resid 415 through 422 Processing helix chain 'C' and resid 477 through 493 removed outlier: 3.950A pdb=" N GLU C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 527 Processing helix chain 'C' and resid 542 through 554 Processing helix chain 'C' and resid 614 through 620 Processing helix chain 'C' and resid 630 through 646 Processing helix chain 'C' and resid 672 through 685 Processing helix chain 'D' and resid 9 through 26 Processing helix chain 'D' and resid 31 through 53 removed outlier: 3.782A pdb=" N GLY D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 64 removed outlier: 3.580A pdb=" N LEU D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 105 Processing helix chain 'D' and resid 116 through 130 Processing helix chain 'D' and resid 145 through 150 removed outlier: 4.526A pdb=" N PHE D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 206 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.804A pdb=" N PHE D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 296 through 303 removed outlier: 3.633A pdb=" N ILE D 301 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 339 removed outlier: 3.867A pdb=" N ALA D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 363 removed outlier: 3.850A pdb=" N PHE D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 381 through 393 Processing helix chain 'D' and resid 415 through 422 Processing helix chain 'D' and resid 477 through 493 removed outlier: 3.950A pdb=" N GLU D 483 " --> pdb=" O ARG D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 527 Processing helix chain 'D' and resid 542 through 554 Processing helix chain 'D' and resid 614 through 620 Processing helix chain 'D' and resid 630 through 646 Processing helix chain 'D' and resid 672 through 685 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 109 removed outlier: 6.288A pdb=" N PHE A 108 " --> pdb=" O MET A 196 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU A 198 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 138 through 140 removed outlier: 4.822A pdb=" N TYR A 169 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR A 154 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N MET A 227 " --> pdb=" O TYR A 154 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 221 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 219 " --> pdb=" O ILE A 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.934A pdb=" N GLU A 448 " --> pdb=" O GLU A 445 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 437 " --> pdb=" O GLY A 456 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU A 438 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE A 371 " --> pdb=" O LEU A 438 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 440 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE A 369 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER A 442 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU A 367 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 397 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 369 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL A 399 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 371 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 396 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE A 426 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 398 " --> pdb=" O ILE A 426 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 345 Processing sheet with id=AA5, first strand: chain 'A' and resid 504 through 505 removed outlier: 3.874A pdb=" N ARG A 594 " --> pdb=" O SER A 609 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE A 585 " --> pdb=" O VAL A 563 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 109 removed outlier: 6.288A pdb=" N PHE B 108 " --> pdb=" O MET B 196 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU B 198 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 140 removed outlier: 4.822A pdb=" N TYR B 169 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR B 154 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N MET B 227 " --> pdb=" O TYR B 154 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 221 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 219 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.934A pdb=" N GLU B 448 " --> pdb=" O GLU B 445 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 437 " --> pdb=" O GLY B 456 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU B 438 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE B 371 " --> pdb=" O LEU B 438 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU B 440 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE B 369 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER B 442 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU B 367 " --> pdb=" O LYS B 395 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR B 397 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 369 " --> pdb=" O THR B 397 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL B 399 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 371 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B 396 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE B 426 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL B 398 " --> pdb=" O ILE B 426 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AB1, first strand: chain 'B' and resid 504 through 505 removed outlier: 3.874A pdb=" N ARG B 594 " --> pdb=" O SER B 609 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE B 585 " --> pdb=" O VAL B 563 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.288A pdb=" N PHE C 108 " --> pdb=" O MET C 196 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU C 198 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 140 removed outlier: 4.822A pdb=" N TYR C 169 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR C 154 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N MET C 227 " --> pdb=" O TYR C 154 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN C 221 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA C 219 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.934A pdb=" N GLU C 448 " --> pdb=" O GLU C 445 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS C 437 " --> pdb=" O GLY C 456 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU C 438 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE C 371 " --> pdb=" O LEU C 438 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU C 440 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 369 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER C 442 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU C 367 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR C 397 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 369 " --> pdb=" O THR C 397 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL C 399 " --> pdb=" O ILE C 369 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE C 371 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL C 396 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE C 426 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL C 398 " --> pdb=" O ILE C 426 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AB6, first strand: chain 'C' and resid 504 through 505 removed outlier: 3.874A pdb=" N ARG C 594 " --> pdb=" O SER C 609 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE C 585 " --> pdb=" O VAL C 563 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 108 through 109 removed outlier: 6.288A pdb=" N PHE D 108 " --> pdb=" O MET D 196 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU D 198 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 138 through 140 removed outlier: 4.822A pdb=" N TYR D 169 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR D 154 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N MET D 227 " --> pdb=" O TYR D 154 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 221 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 219 " --> pdb=" O ILE D 162 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 341 through 345 removed outlier: 3.934A pdb=" N GLU D 448 " --> pdb=" O GLU D 445 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS D 437 " --> pdb=" O GLY D 456 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU D 438 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE D 371 " --> pdb=" O LEU D 438 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU D 440 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE D 369 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N SER D 442 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N LEU D 367 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR D 397 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 369 " --> pdb=" O THR D 397 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N VAL D 399 " --> pdb=" O ILE D 369 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE D 371 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL D 396 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE D 426 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL D 398 " --> pdb=" O ILE D 426 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 341 through 345 Processing sheet with id=AC2, first strand: chain 'D' and resid 504 through 505 removed outlier: 3.874A pdb=" N ARG D 594 " --> pdb=" O SER D 609 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE D 585 " --> pdb=" O VAL D 563 " (cutoff:3.500A) 1024 hydrogen bonds defined for protein. 2952 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6788 1.34 - 1.46: 3544 1.46 - 1.57: 10640 1.57 - 1.69: 24 1.69 - 1.81: 96 Bond restraints: 21092 Sorted by residual: bond pdb=" O13 7TT C 701 " pdb=" P14 7TT C 701 " ideal model delta sigma weight residual 1.700 1.619 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O13 7TT D 701 " pdb=" P14 7TT D 701 " ideal model delta sigma weight residual 1.700 1.619 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O13 7TT B 701 " pdb=" P14 7TT B 701 " ideal model delta sigma weight residual 1.700 1.619 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O13 7TT A 701 " pdb=" P14 7TT A 701 " ideal model delta sigma weight residual 1.700 1.619 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O07 7TT A 701 " pdb=" P05 7TT A 701 " ideal model delta sigma weight residual 1.696 1.620 0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 21087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 28136 1.75 - 3.49: 330 3.49 - 5.24: 46 5.24 - 6.99: 4 6.99 - 8.73: 8 Bond angle restraints: 28524 Sorted by residual: angle pdb=" N ARG B 320 " pdb=" CA ARG B 320 " pdb=" C ARG B 320 " ideal model delta sigma weight residual 109.40 102.52 6.88 1.63e+00 3.76e-01 1.78e+01 angle pdb=" N ARG A 320 " pdb=" CA ARG A 320 " pdb=" C ARG A 320 " ideal model delta sigma weight residual 109.40 102.52 6.88 1.63e+00 3.76e-01 1.78e+01 angle pdb=" N ARG D 320 " pdb=" CA ARG D 320 " pdb=" C ARG D 320 " ideal model delta sigma weight residual 109.40 102.52 6.88 1.63e+00 3.76e-01 1.78e+01 angle pdb=" N ARG C 320 " pdb=" CA ARG C 320 " pdb=" C ARG C 320 " ideal model delta sigma weight residual 109.40 102.52 6.88 1.63e+00 3.76e-01 1.78e+01 angle pdb=" N ILE D 322 " pdb=" CA ILE D 322 " pdb=" CB ILE D 322 " ideal model delta sigma weight residual 111.23 102.50 8.73 2.36e+00 1.80e-01 1.37e+01 ... (remaining 28519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.53: 11912 28.53 - 57.06: 912 57.06 - 85.58: 36 85.58 - 114.11: 12 114.11 - 142.64: 8 Dihedral angle restraints: 12880 sinusoidal: 5480 harmonic: 7400 Sorted by residual: dihedral pdb=" O10 7TT D 701 " pdb=" O13 7TT D 701 " pdb=" P11 7TT D 701 " pdb=" P14 7TT D 701 " ideal model delta sinusoidal sigma weight residual -82.99 59.65 -142.64 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" O10 7TT A 701 " pdb=" O13 7TT A 701 " pdb=" P11 7TT A 701 " pdb=" P14 7TT A 701 " ideal model delta sinusoidal sigma weight residual -82.99 59.65 -142.64 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" O10 7TT B 701 " pdb=" O13 7TT B 701 " pdb=" P11 7TT B 701 " pdb=" P14 7TT B 701 " ideal model delta sinusoidal sigma weight residual -82.99 59.65 -142.64 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 12877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2512 0.045 - 0.090: 420 0.090 - 0.135: 208 0.135 - 0.180: 4 0.180 - 0.225: 8 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA ILE B 322 " pdb=" N ILE B 322 " pdb=" C ILE B 322 " pdb=" CB ILE B 322 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE D 322 " pdb=" N ILE D 322 " pdb=" C ILE D 322 " pdb=" CB ILE D 322 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE C 322 " pdb=" N ILE C 322 " pdb=" C ILE C 322 " pdb=" CB ILE C 322 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 3149 not shown) Planarity restraints: 3644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 600 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ASN C 600 " 0.051 2.00e-02 2.50e+03 pdb=" O ASN C 600 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY C 601 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 600 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ASN A 600 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN A 600 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY A 601 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 600 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C ASN D 600 " -0.051 2.00e-02 2.50e+03 pdb=" O ASN D 600 " 0.020 2.00e-02 2.50e+03 pdb=" N GLY D 601 " 0.017 2.00e-02 2.50e+03 ... (remaining 3641 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 5088 2.80 - 3.33: 17936 3.33 - 3.85: 32274 3.85 - 4.38: 40096 4.38 - 4.90: 69732 Nonbonded interactions: 165126 Sorted by model distance: nonbonded pdb=" ND2 ASN A 331 " pdb=" O GLY D 213 " model vdw 2.278 3.120 nonbonded pdb=" ND2 ASN B 331 " pdb=" O GLY C 213 " model vdw 2.278 3.120 nonbonded pdb=" O GLY B 213 " pdb=" ND2 ASN C 331 " model vdw 2.278 3.120 nonbonded pdb=" O GLY A 213 " pdb=" ND2 ASN D 331 " model vdw 2.278 3.120 nonbonded pdb=" OG SER A 506 " pdb=" OG SER A 510 " model vdw 2.297 3.040 ... (remaining 165121 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.640 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.100 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 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 : 0.003 0.081 21092 Z= 0.137 Angle : 0.481 8.732 28524 Z= 0.258 Chirality : 0.041 0.225 3152 Planarity : 0.003 0.034 3644 Dihedral : 18.154 142.638 8080 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 23.80 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.27 (0.17), residues: 2440 helix: 0.83 (0.15), residues: 1024 sheet: 0.33 (0.25), residues: 472 loop : -0.51 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 665 TYR 0.011 0.001 TYR D 374 PHE 0.016 0.001 PHE A 214 TRP 0.007 0.001 TRP C 613 HIS 0.001 0.000 HIS B 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (21092) covalent geometry : angle 0.48129 / 0.26 (28524) hydrogen bonds : bond 0.23499 / 15.49 ( 1000) hydrogen bonds : angle 7.37669 / 5.32 ( 2952) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.716 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.1700 time to fit residues: 64.1622 Evaluate side-chains 248 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 310 ASN A 686 GLN B 121 ASN B 310 ASN B 686 GLN C 121 ASN C 310 ASN C 686 GLN D 121 ASN D 310 ASN D 686 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.123253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.100575 restraints weight = 24993.439| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.83 r_work: 0.2834 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 21092 Z= 0.174 Angle : 0.492 5.464 28524 Z= 0.260 Chirality : 0.043 0.144 3152 Planarity : 0.004 0.028 3644 Dihedral : 9.901 150.104 2888 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.66 % Allowed : 21.49 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 0.87 (0.17), residues: 2440 helix: 1.76 (0.15), residues: 1040 sheet: 0.20 (0.24), residues: 468 loop : -0.52 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 665 TYR 0.012 0.001 TYR D 471 PHE 0.027 0.002 PHE C 439 TRP 0.006 0.001 TRP C 14 HIS 0.004 0.001 HIS B 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (21092) covalent geometry : angle 0.49234 / 0.26 (28524) hydrogen bonds : bond 0.04765 / 3.15 ( 1000) hydrogen bonds : angle 4.77969 / 3.38 ( 2952) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 256 time to evaluate : 0.796 Fit side-chains REVERT: A 470 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: A 682 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7567 (ttpp) REVERT: B 470 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8256 (m-30) REVERT: B 682 LYS cc_start: 0.7963 (ttmt) cc_final: 0.7579 (ttpp) REVERT: C 470 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: C 682 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7594 (ttpp) REVERT: D 470 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8245 (m-30) REVERT: D 682 LYS cc_start: 0.7957 (ttmt) cc_final: 0.7578 (ttpp) outliers start: 60 outliers final: 32 residues processed: 300 average time/residue: 0.1666 time to fit residues: 72.9653 Evaluate side-chains 284 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 656 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 54 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 234 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN D 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.124435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.101559 restraints weight = 24847.613| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.85 r_work: 0.2832 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21092 Z= 0.136 Angle : 0.447 5.392 28524 Z= 0.237 Chirality : 0.042 0.147 3152 Planarity : 0.003 0.027 3644 Dihedral : 9.809 156.407 2888 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.95 % Allowed : 21.67 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.24 (0.17), residues: 2440 helix: 2.22 (0.16), residues: 1040 sheet: 0.31 (0.25), residues: 468 loop : -0.49 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 132 TYR 0.010 0.001 TYR B 471 PHE 0.025 0.001 PHE C 439 TRP 0.005 0.001 TRP C 14 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (21092) covalent geometry : angle 0.44747 / 0.24 (28524) hydrogen bonds : bond 0.04070 / 2.67 ( 1000) hydrogen bonds : angle 4.42265 / 3.12 ( 2952) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 252 time to evaluate : 0.735 Fit side-chains REVERT: A 381 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7014 (mtm180) REVERT: A 682 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7549 (ttpp) REVERT: B 381 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.6992 (mtm180) REVERT: B 682 LYS cc_start: 0.7959 (ttmt) cc_final: 0.7554 (ttpp) REVERT: C 381 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7011 (mtm180) REVERT: C 682 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7551 (ttpp) REVERT: D 381 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.6999 (mtm180) REVERT: D 682 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7549 (ttpp) outliers start: 44 outliers final: 36 residues processed: 280 average time/residue: 0.1901 time to fit residues: 75.5449 Evaluate side-chains 284 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 244 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 129 GLN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 163 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 165 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 201 optimal weight: 0.0970 chunk 195 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 686 GLN B 686 GLN C 686 GLN D 686 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.125867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.103009 restraints weight = 24844.385| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.85 r_work: 0.2852 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21092 Z= 0.107 Angle : 0.422 5.782 28524 Z= 0.224 Chirality : 0.041 0.156 3152 Planarity : 0.003 0.027 3644 Dihedral : 9.754 162.260 2888 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.60 % Allowed : 21.85 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.46 (0.17), residues: 2440 helix: 2.44 (0.16), residues: 1040 sheet: 0.32 (0.24), residues: 500 loop : -0.39 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 53 TYR 0.008 0.001 TYR C 471 PHE 0.025 0.001 PHE D 439 TRP 0.006 0.001 TRP D 14 HIS 0.002 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (21092) covalent geometry : angle 0.42175 / 0.22 (28524) hydrogen bonds : bond 0.03477 / 2.29 ( 1000) hydrogen bonds : angle 4.18470 / 2.95 ( 2952) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 0.783 Fit side-chains REVERT: A 381 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.6961 (mtm180) REVERT: A 682 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7501 (ttpp) REVERT: B 381 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.6943 (mtm180) REVERT: B 682 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7506 (ttpp) REVERT: C 381 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.6963 (mtm180) REVERT: C 682 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7508 (ttpp) REVERT: D 381 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.6950 (mtm180) REVERT: D 682 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7499 (ttpp) outliers start: 36 outliers final: 24 residues processed: 276 average time/residue: 0.1855 time to fit residues: 72.7720 Evaluate side-chains 264 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 26 optimal weight: 0.0570 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN C 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.095350 restraints weight = 25349.646| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.81 r_work: 0.2794 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 21092 Z= 0.217 Angle : 0.510 6.035 28524 Z= 0.266 Chirality : 0.044 0.155 3152 Planarity : 0.004 0.043 3644 Dihedral : 10.040 170.319 2888 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.11 % Allowed : 21.31 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.22 (0.17), residues: 2440 helix: 2.24 (0.16), residues: 1040 sheet: 0.28 (0.24), residues: 488 loop : -0.57 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 665 TYR 0.011 0.001 TYR D 471 PHE 0.027 0.002 PHE B 439 TRP 0.007 0.001 TRP D 323 HIS 0.005 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.22 (21092) covalent geometry : angle 0.50970 / 0.27 (28524) hydrogen bonds : bond 0.04671 / 3.06 ( 1000) hydrogen bonds : angle 4.45074 / 3.14 ( 2952) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 240 time to evaluate : 0.799 Fit side-chains REVERT: A 59 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7446 (mtm180) REVERT: A 381 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7025 (mtm180) REVERT: A 444 LYS cc_start: 0.9244 (tttp) cc_final: 0.8979 (tptp) REVERT: A 682 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7590 (ttpp) REVERT: B 59 ARG cc_start: 0.7729 (mtm110) cc_final: 0.7446 (mtm180) REVERT: B 381 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7027 (mtm180) REVERT: B 444 LYS cc_start: 0.9248 (tttp) cc_final: 0.8982 (tptp) REVERT: B 682 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7599 (ttpp) REVERT: C 59 ARG cc_start: 0.7715 (mtm110) cc_final: 0.7428 (mtm180) REVERT: C 381 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7021 (mtm180) REVERT: C 444 LYS cc_start: 0.9251 (tttp) cc_final: 0.8987 (tptp) REVERT: C 682 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7608 (ttpp) REVERT: D 59 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7435 (mtm180) REVERT: D 381 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7018 (mtm180) REVERT: D 444 LYS cc_start: 0.9243 (tttp) cc_final: 0.8972 (tptp) REVERT: D 682 LYS cc_start: 0.8007 (ttmt) cc_final: 0.7603 (ttpp) outliers start: 70 outliers final: 48 residues processed: 298 average time/residue: 0.1847 time to fit residues: 78.1865 Evaluate side-chains 280 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 656 LYS Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 656 LYS Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 110 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 656 LYS Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 656 LYS Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 18 optimal weight: 0.5980 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 246 optimal weight: 0.0010 chunk 102 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.125017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.102328 restraints weight = 24888.780| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.81 r_work: 0.2856 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21092 Z= 0.090 Angle : 0.415 6.220 28524 Z= 0.221 Chirality : 0.041 0.172 3152 Planarity : 0.003 0.043 3644 Dihedral : 9.904 176.183 2888 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.13 % Allowed : 21.67 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.51 (0.17), residues: 2440 helix: 2.54 (0.16), residues: 1040 sheet: 0.30 (0.24), residues: 500 loop : -0.42 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 665 TYR 0.007 0.001 TYR D 596 PHE 0.024 0.001 PHE C 439 TRP 0.008 0.001 TRP C 14 HIS 0.001 0.000 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (21092) covalent geometry : angle 0.41514 / 0.22 (28524) hydrogen bonds : bond 0.03197 / 2.11 ( 1000) hydrogen bonds : angle 4.03522 / 2.84 ( 2952) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.781 Fit side-chains REVERT: A 59 ARG cc_start: 0.7738 (mtm110) cc_final: 0.7447 (mtm180) REVERT: A 381 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.6922 (mtm180) REVERT: A 438 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8671 (mt) REVERT: A 444 LYS cc_start: 0.9156 (tttp) cc_final: 0.8755 (tppt) REVERT: B 59 ARG cc_start: 0.7731 (mtm110) cc_final: 0.7443 (mtm180) REVERT: B 381 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6905 (mtm180) REVERT: B 438 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8667 (mt) REVERT: B 444 LYS cc_start: 0.9163 (tttp) cc_final: 0.8758 (tppt) REVERT: C 59 ARG cc_start: 0.7708 (mtm110) cc_final: 0.7418 (mtm180) REVERT: C 381 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.6912 (mtm180) REVERT: C 438 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8668 (mt) REVERT: C 444 LYS cc_start: 0.9161 (tttp) cc_final: 0.8753 (tppt) REVERT: D 59 ARG cc_start: 0.7720 (mtm110) cc_final: 0.7429 (mtm180) REVERT: D 381 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.6897 (mtm180) REVERT: D 438 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8667 (mt) REVERT: D 444 LYS cc_start: 0.9158 (tttp) cc_final: 0.8752 (tppt) outliers start: 48 outliers final: 40 residues processed: 284 average time/residue: 0.1886 time to fit residues: 76.4739 Evaluate side-chains 284 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 239 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 167 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS A 686 GLN B 321 HIS B 686 GLN C 321 HIS C 686 GLN D 321 HIS D 686 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103461 restraints weight = 24788.115| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.82 r_work: 0.2846 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21092 Z= 0.112 Angle : 0.430 6.317 28524 Z= 0.228 Chirality : 0.041 0.167 3152 Planarity : 0.003 0.027 3644 Dihedral : 9.928 176.958 2888 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.66 % Allowed : 21.49 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.57 (0.17), residues: 2440 helix: 2.60 (0.16), residues: 1040 sheet: 0.32 (0.24), residues: 500 loop : -0.37 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 665 TYR 0.009 0.001 TYR B 205 PHE 0.024 0.001 PHE D 439 TRP 0.005 0.001 TRP D 14 HIS 0.002 0.000 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (21092) covalent geometry : angle 0.43002 / 0.23 (28524) hydrogen bonds : bond 0.03398 / 2.24 ( 1000) hydrogen bonds : angle 4.04264 / 2.85 ( 2952) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 238 time to evaluate : 0.900 Fit side-chains REVERT: A 59 ARG cc_start: 0.7757 (mtm110) cc_final: 0.7491 (mtm180) REVERT: A 381 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6936 (mtm180) REVERT: A 438 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8672 (mt) REVERT: A 444 LYS cc_start: 0.9162 (tttp) cc_final: 0.8766 (tppt) REVERT: B 59 ARG cc_start: 0.7751 (mtm110) cc_final: 0.7490 (mtm180) REVERT: B 381 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6915 (mtm180) REVERT: B 438 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B 444 LYS cc_start: 0.9167 (tttp) cc_final: 0.8769 (tppt) REVERT: C 59 ARG cc_start: 0.7728 (mtm110) cc_final: 0.7463 (mtm180) REVERT: C 381 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.6930 (mtm180) REVERT: C 438 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8674 (mt) REVERT: C 444 LYS cc_start: 0.9169 (tttp) cc_final: 0.8765 (tppt) REVERT: D 59 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7475 (mtm180) REVERT: D 381 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.6915 (mtm180) REVERT: D 438 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8673 (mt) REVERT: D 444 LYS cc_start: 0.9162 (tttp) cc_final: 0.8764 (tppt) outliers start: 60 outliers final: 44 residues processed: 290 average time/residue: 0.1844 time to fit residues: 75.9818 Evaluate side-chains 286 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 234 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 44 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 232 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS B 321 HIS C 310 ASN C 321 HIS D 321 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098236 restraints weight = 25008.881| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.83 r_work: 0.2823 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 21092 Z= 0.136 Angle : 0.447 6.705 28524 Z= 0.236 Chirality : 0.042 0.181 3152 Planarity : 0.003 0.028 3644 Dihedral : 9.892 168.529 2888 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.75 % Allowed : 21.45 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.50 (0.17), residues: 2440 helix: 2.53 (0.16), residues: 1040 sheet: 0.24 (0.24), residues: 500 loop : -0.38 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 665 TYR 0.009 0.001 TYR A 471 PHE 0.025 0.001 PHE C 439 TRP 0.005 0.001 TRP A 14 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (21092) covalent geometry : angle 0.44721 / 0.24 (28524) hydrogen bonds : bond 0.03729 / 2.45 ( 1000) hydrogen bonds : angle 4.12447 / 2.90 ( 2952) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 248 time to evaluate : 0.841 Fit side-chains REVERT: A 59 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7462 (mtm180) REVERT: A 338 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8319 (tp30) REVERT: A 381 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6946 (mtm180) REVERT: A 438 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8736 (mt) REVERT: A 444 LYS cc_start: 0.9165 (tttp) cc_final: 0.8757 (tppt) REVERT: A 682 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7534 (ttpp) REVERT: B 59 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7462 (mtm180) REVERT: B 338 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8324 (tp30) REVERT: B 381 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.6928 (mtm180) REVERT: B 438 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8737 (mt) REVERT: B 444 LYS cc_start: 0.9164 (tttp) cc_final: 0.8755 (tppt) REVERT: B 682 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7534 (ttpp) REVERT: C 59 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7434 (mtm180) REVERT: C 338 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8302 (tp30) REVERT: C 381 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.6936 (mtm180) REVERT: C 438 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8736 (mt) REVERT: C 444 LYS cc_start: 0.9166 (tttp) cc_final: 0.8757 (tppt) REVERT: C 682 LYS cc_start: 0.7940 (ttmt) cc_final: 0.7531 (ttpp) REVERT: D 59 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7437 (mtm180) REVERT: D 338 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8321 (tp30) REVERT: D 381 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.6931 (mtm180) REVERT: D 438 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8741 (mt) REVERT: D 444 LYS cc_start: 0.9163 (tttp) cc_final: 0.8755 (tppt) REVERT: D 682 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7529 (ttpp) outliers start: 62 outliers final: 46 residues processed: 302 average time/residue: 0.2069 time to fit residues: 88.9575 Evaluate side-chains 302 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 40 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS B 321 HIS C 321 HIS D 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.100090 restraints weight = 24879.839| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.82 r_work: 0.2836 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21092 Z= 0.139 Angle : 0.450 6.808 28524 Z= 0.240 Chirality : 0.042 0.186 3152 Planarity : 0.003 0.028 3644 Dihedral : 9.778 168.723 2888 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.11 % Allowed : 21.23 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.50 (0.17), residues: 2440 helix: 2.53 (0.16), residues: 1040 sheet: 0.27 (0.24), residues: 500 loop : -0.38 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 665 TYR 0.009 0.001 TYR A 205 PHE 0.026 0.001 PHE C 439 TRP 0.005 0.001 TRP C 14 HIS 0.003 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (21092) covalent geometry : angle 0.44989 / 0.24 (28524) hydrogen bonds : bond 0.03698 / 2.43 ( 1000) hydrogen bonds : angle 4.11400 / 2.90 ( 2952) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 236 time to evaluate : 0.899 Fit side-chains REVERT: A 59 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7472 (mtm180) REVERT: A 338 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: A 381 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.6953 (mtm180) REVERT: A 438 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8749 (mt) REVERT: A 444 LYS cc_start: 0.9165 (tttp) cc_final: 0.8762 (tppt) REVERT: A 682 LYS cc_start: 0.7989 (ttmt) cc_final: 0.7577 (ttpp) REVERT: B 59 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7487 (mtm180) REVERT: B 338 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8326 (tp30) REVERT: B 381 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.6934 (mtm180) REVERT: B 438 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8750 (mt) REVERT: B 444 LYS cc_start: 0.9163 (tttp) cc_final: 0.8756 (tppt) REVERT: B 682 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7574 (ttpp) REVERT: C 59 ARG cc_start: 0.7704 (mtm110) cc_final: 0.7459 (mtm180) REVERT: C 338 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8308 (tp30) REVERT: C 381 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.6945 (mtm180) REVERT: C 438 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8750 (mt) REVERT: C 444 LYS cc_start: 0.9170 (tttp) cc_final: 0.8763 (tppt) REVERT: C 682 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7565 (ttpp) REVERT: D 59 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7452 (mtm180) REVERT: D 338 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8314 (tp30) REVERT: D 381 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.6946 (mtm180) REVERT: D 438 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8750 (mt) REVERT: D 444 LYS cc_start: 0.9161 (tttp) cc_final: 0.8756 (tppt) REVERT: D 682 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7565 (ttpp) outliers start: 70 outliers final: 54 residues processed: 294 average time/residue: 0.2055 time to fit residues: 85.5551 Evaluate side-chains 298 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 217 optimal weight: 0.0020 chunk 229 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 198 optimal weight: 0.0670 chunk 236 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS B 321 HIS C 321 HIS D 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.127718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.105074 restraints weight = 24777.487| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.82 r_work: 0.2896 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21092 Z= 0.081 Angle : 0.409 6.827 28524 Z= 0.222 Chirality : 0.040 0.184 3152 Planarity : 0.003 0.025 3644 Dihedral : 9.487 171.053 2888 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.22 % Allowed : 22.29 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.77 (0.18), residues: 2440 helix: 2.75 (0.16), residues: 1044 sheet: 0.44 (0.24), residues: 500 loop : -0.27 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 665 TYR 0.007 0.001 TYR D 471 PHE 0.023 0.001 PHE B 439 TRP 0.008 0.001 TRP C 14 HIS 0.001 0.000 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.08 (21092) covalent geometry : angle 0.40906 / 0.22 (28524) hydrogen bonds : bond 0.02758 / 1.82 ( 1000) hydrogen bonds : angle 3.83444 / 2.69 ( 2952) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4880 Ramachandran restraints generated. 2440 Oldfield, 0 Emsley, 2440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 0.576 Fit side-chains REVERT: A 59 ARG cc_start: 0.7776 (mtm110) cc_final: 0.7520 (mtm180) REVERT: A 381 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6963 (mtm180) REVERT: A 438 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8693 (mt) REVERT: A 444 LYS cc_start: 0.9118 (tttp) cc_final: 0.8772 (tppt) REVERT: A 600 ASN cc_start: 0.8549 (t0) cc_final: 0.8169 (t0) REVERT: B 59 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7511 (mtm180) REVERT: B 381 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6955 (mtm180) REVERT: B 438 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8690 (mt) REVERT: B 444 LYS cc_start: 0.9126 (tttp) cc_final: 0.8778 (tppt) REVERT: B 600 ASN cc_start: 0.8546 (t0) cc_final: 0.8157 (t0) REVERT: C 59 ARG cc_start: 0.7752 (mtm110) cc_final: 0.7498 (mtm180) REVERT: C 381 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.6955 (mtm180) REVERT: C 438 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8697 (mt) REVERT: C 444 LYS cc_start: 0.9121 (tttp) cc_final: 0.8776 (tppt) REVERT: C 600 ASN cc_start: 0.8548 (t0) cc_final: 0.8165 (t0) REVERT: D 59 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7511 (mtm180) REVERT: D 381 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.6952 (mtm180) REVERT: D 438 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8690 (mt) REVERT: D 444 LYS cc_start: 0.9122 (tttp) cc_final: 0.8779 (tppt) REVERT: D 600 ASN cc_start: 0.8542 (t0) cc_final: 0.8157 (t0) outliers start: 50 outliers final: 38 residues processed: 294 average time/residue: 0.2054 time to fit residues: 84.9256 Evaluate side-chains 282 residues out of total 2252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 PHE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 381 ARG Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 609 SER Chi-restraints excluded: chain A residue 626 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 38 PHE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 381 ARG Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 626 THR Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain C residue 38 PHE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 381 ARG Chi-restraints excluded: chain C residue 438 LEU Chi-restraints excluded: chain C residue 467 LEU Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 626 THR Chi-restraints excluded: chain C residue 657 GLU Chi-restraints excluded: chain D residue 38 PHE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 381 ARG Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 609 SER Chi-restraints excluded: chain D residue 626 THR Chi-restraints excluded: chain D residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 233 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 HIS B 321 HIS C 321 HIS D 321 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.094480 restraints weight = 25328.903| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.82 r_work: 0.2784 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 21092 Z= 0.264 Angle : 0.557 6.780 28524 Z= 0.292 Chirality : 0.045 0.177 3152 Planarity : 0.004 0.033 3644 Dihedral : 9.977 174.189 2888 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.49 % Allowed : 22.20 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 1.30 (0.17), residues: 2440 helix: 2.31 (0.16), residues: 1040 sheet: 0.32 (0.24), residues: 488 loop : -0.52 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 168 TYR 0.013 0.002 TYR B 42 PHE 0.030 0.002 PHE C 439 TRP 0.007 0.001 TRP A 323 HIS 0.006 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00661 / 0.26 (21092) covalent geometry : angle 0.55742 / 0.29 (28524) hydrogen bonds : bond 0.04962 / 3.25 ( 1000) hydrogen bonds : angle 4.43610 / 3.12 ( 2952) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4774.47 seconds wall clock time: 82 minutes 31.01 seconds (4951.01 seconds total)