Starting phenix.real_space_refine on Sat Sep 12 11:49:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.cif" model { file = "/net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ayf_7019/09_2026/6ayf_7019.map" } resolution = 3.62 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= 0.008 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 10360 2.51 5 N 2504 2.21 5 O 2788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15780 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "B" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "C" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "D" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3917 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 9, 'TRANS': 466} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.28, per 1000 atoms: 0.21 Number of scatterers: 15780 At special positions: 0 Unit cell: (108.378, 108.378, 115.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 2788 8.00 N 2504 7.00 C 10360 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 138 " " NAG A 602 " - " ASN A 172 " " NAG B 601 " - " ASN B 138 " " NAG B 602 " - " ASN B 172 " " NAG C 601 " - " ASN C 138 " " NAG C 602 " - " ASN C 172 " " NAG D 601 " - " ASN D 138 " " NAG D 602 " - " ASN D 172 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 725.9 milliseconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 64.8% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 33 through 46 removed outlier: 4.018A pdb=" N PHE A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 3.875A pdb=" N ARG A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY A 57 " --> pdb=" O PHE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 103 removed outlier: 3.506A pdb=" N GLN A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.908A pdb=" N VAL A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 325 removed outlier: 3.608A pdb=" N ALA A 290 " --> pdb=" O MET A 286 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS A 324 " --> pdb=" O PHE A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 338 removed outlier: 3.759A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 365 removed outlier: 3.693A pdb=" N MET A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.564A pdb=" N LEU A 376 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 399 through 435 removed outlier: 3.660A pdb=" N GLN A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Proline residue: A 410 - end of helix removed outlier: 4.075A pdb=" N ARG A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A 422 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 456 Processing helix chain 'A' and resid 460 through 466 Processing helix chain 'A' and resid 471 through 490 Processing helix chain 'A' and resid 490 through 514 Processing helix chain 'A' and resid 519 through 525 Processing helix chain 'B' and resid 34 through 46 removed outlier: 4.016A pdb=" N PHE B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.876A pdb=" N ARG B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY B 57 " --> pdb=" O PHE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 103 removed outlier: 3.504A pdb=" N GLN B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 135 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.911A pdb=" N VAL B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 325 removed outlier: 3.605A pdb=" N ALA B 290 " --> pdb=" O MET B 286 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N CYS B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU B 323 " --> pdb=" O ASN B 319 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 338 removed outlier: 3.767A pdb=" N PHE B 337 " --> pdb=" O ASP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 365 removed outlier: 3.704A pdb=" N MET B 344 " --> pdb=" O GLY B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.558A pdb=" N LEU B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 394 Processing helix chain 'B' and resid 399 through 435 removed outlier: 3.655A pdb=" N GLN B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Proline residue: B 410 - end of helix removed outlier: 4.083A pdb=" N ARG B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 422 " --> pdb=" O CYS B 418 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N CYS B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 456 Processing helix chain 'B' and resid 460 through 467 removed outlier: 3.844A pdb=" N MET B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 490 Processing helix chain 'B' and resid 490 through 514 Processing helix chain 'B' and resid 519 through 525 Processing helix chain 'C' and resid 34 through 46 removed outlier: 4.019A pdb=" N PHE C 44 " --> pdb=" O ARG C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.876A pdb=" N ARG C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 57 " --> pdb=" O PHE C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 103 removed outlier: 3.505A pdb=" N GLN C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 83 " --> pdb=" O LEU C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 135 Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.908A pdb=" N VAL C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 325 removed outlier: 3.605A pdb=" N ALA C 290 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 310 " --> pdb=" O SER C 306 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LEU C 323 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS C 324 " --> pdb=" O PHE C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 338 removed outlier: 3.763A pdb=" N PHE C 337 " --> pdb=" O ASP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 365 removed outlier: 3.702A pdb=" N MET C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 388 removed outlier: 3.562A pdb=" N LEU C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 394 Processing helix chain 'C' and resid 399 through 435 removed outlier: 3.657A pdb=" N GLN C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Proline residue: C 410 - end of helix removed outlier: 4.082A pdb=" N ARG C 414 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 422 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 456 Processing helix chain 'C' and resid 460 through 466 Processing helix chain 'C' and resid 471 through 490 Processing helix chain 'C' and resid 490 through 514 Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'D' and resid 34 through 46 removed outlier: 4.019A pdb=" N PHE D 44 " --> pdb=" O ARG D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 removed outlier: 3.874A pdb=" N ARG D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY D 57 " --> pdb=" O PHE D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 103 removed outlier: 3.510A pdb=" N GLN D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.914A pdb=" N VAL D 230 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 325 removed outlier: 3.607A pdb=" N ALA D 290 " --> pdb=" O MET D 286 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 310 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU D 323 " --> pdb=" O ASN D 319 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS D 324 " --> pdb=" O PHE D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 338 removed outlier: 3.743A pdb=" N PHE D 337 " --> pdb=" O ASP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 365 removed outlier: 3.693A pdb=" N MET D 344 " --> pdb=" O GLY D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 388 removed outlier: 3.556A pdb=" N LEU D 376 " --> pdb=" O VAL D 372 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 394 Processing helix chain 'D' and resid 399 through 435 removed outlier: 3.659A pdb=" N GLN D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 409 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Proline residue: D 410 - end of helix removed outlier: 4.084A pdb=" N ARG D 414 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D 422 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS D 429 " --> pdb=" O GLY D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 456 Processing helix chain 'D' and resid 460 through 466 Processing helix chain 'D' and resid 471 through 490 removed outlier: 3.514A pdb=" N ARG D 479 " --> pdb=" O TRP D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 490 through 514 Processing helix chain 'D' and resid 519 through 525 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 6.930A pdb=" N LEU A 213 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 163 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE A 158 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 146 removed outlier: 6.930A pdb=" N LEU A 213 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 163 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N HIS A 161 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU A 182 " --> pdb=" O HIS A 161 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N TYR A 163 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU A 180 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 165 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 274 removed outlier: 6.501A pdb=" N HIS A 273 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 165 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU B 180 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N TYR B 163 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU B 182 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS B 161 " --> pdb=" O GLU B 182 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR B 163 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU B 213 " --> pdb=" O TYR B 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 115 through 116 removed outlier: 6.929A pdb=" N LEU B 213 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR B 163 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE B 158 " --> pdb=" O PHE B 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 272 through 274 removed outlier: 6.474A pdb=" N HIS B 273 " --> pdb=" O ILE C 177 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG C 165 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLU C 180 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR C 163 " --> pdb=" O GLU C 180 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU C 182 " --> pdb=" O HIS C 161 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS C 161 " --> pdb=" O GLU C 182 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR C 163 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU C 213 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 115 through 116 removed outlier: 6.926A pdb=" N LEU C 213 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR C 163 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 158 " --> pdb=" O PHE C 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 272 through 274 removed outlier: 6.485A pdb=" N HIS C 273 " --> pdb=" O ILE D 177 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG D 165 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU D 180 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR D 163 " --> pdb=" O GLU D 180 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU D 182 " --> pdb=" O HIS D 161 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N HIS D 161 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR D 163 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 213 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 115 through 116 removed outlier: 6.929A pdb=" N LEU D 213 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR D 163 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE D 158 " --> pdb=" O PHE D 186 " (cutoff:3.500A) 1050 hydrogen bonds defined for protein. 3078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4798 1.34 - 1.46: 3933 1.46 - 1.58: 7217 1.58 - 1.70: 0 1.70 - 1.82: 200 Bond restraints: 16148 Sorted by residual: bond pdb=" NE ARG D 479 " pdb=" CZ ARG D 479 " ideal model delta sigma weight residual 1.326 1.293 0.033 1.10e-02 8.26e+03 8.81e+00 bond pdb=" C1 NAG D 602 " pdb=" O5 NAG D 602 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.74e+00 bond pdb=" C1 NAG C 602 " pdb=" O5 NAG C 602 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" C1 NAG A 602 " pdb=" O5 NAG A 602 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C1 NAG B 602 " pdb=" O5 NAG B 602 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.19e+00 ... (remaining 16143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 20779 1.72 - 3.45: 879 3.45 - 5.17: 124 5.17 - 6.90: 45 6.90 - 8.62: 5 Bond angle restraints: 21832 Sorted by residual: angle pdb=" CA ARG C 479 " pdb=" CB ARG C 479 " pdb=" CG ARG C 479 " ideal model delta sigma weight residual 114.10 106.60 7.50 2.00e+00 2.50e-01 1.41e+01 angle pdb=" NE ARG D 479 " pdb=" CZ ARG D 479 " pdb=" NH1 ARG D 479 " ideal model delta sigma weight residual 121.50 118.14 3.36 1.00e+00 1.00e+00 1.13e+01 angle pdb=" C PHE A 415 " pdb=" N CYS A 416 " pdb=" CA CYS A 416 " ideal model delta sigma weight residual 120.54 124.96 -4.42 1.35e+00 5.49e-01 1.07e+01 angle pdb=" NE ARG C 479 " pdb=" CZ ARG C 479 " pdb=" NH1 ARG C 479 " ideal model delta sigma weight residual 121.50 118.27 3.23 1.00e+00 1.00e+00 1.04e+01 angle pdb=" C PHE C 415 " pdb=" N CYS C 416 " pdb=" CA CYS C 416 " ideal model delta sigma weight residual 120.54 124.67 -4.13 1.35e+00 5.49e-01 9.37e+00 ... (remaining 21827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 7908 14.75 - 29.50: 1121 29.50 - 44.26: 326 44.26 - 59.01: 77 59.01 - 73.76: 20 Dihedral angle restraints: 9452 sinusoidal: 3804 harmonic: 5648 Sorted by residual: dihedral pdb=" CA ASP D 333 " pdb=" C ASP D 333 " pdb=" N GLN D 334 " pdb=" CA GLN D 334 " ideal model delta harmonic sigma weight residual 180.00 154.87 25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ASP A 333 " pdb=" C ASP A 333 " pdb=" N GLN A 334 " pdb=" CA GLN A 334 " ideal model delta harmonic sigma weight residual 180.00 155.15 24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASP B 333 " pdb=" C ASP B 333 " pdb=" N GLN B 334 " pdb=" CA GLN B 334 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 9449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2351 0.094 - 0.187: 133 0.187 - 0.281: 0 0.281 - 0.374: 4 0.374 - 0.468: 4 Chirality restraints: 2492 Sorted by residual: chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 138 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 138 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 138 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 2489 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 44 " -0.028 2.00e-02 2.50e+03 2.22e-02 8.63e+00 pdb=" CG PHE B 44 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 44 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 44 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 44 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 44 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE B 44 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 44 " 0.028 2.00e-02 2.50e+03 2.21e-02 8.52e+00 pdb=" CG PHE D 44 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE D 44 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 44 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 44 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 44 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE D 44 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 44 " 0.028 2.00e-02 2.50e+03 2.19e-02 8.39e+00 pdb=" CG PHE A 44 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 44 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 44 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 44 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 44 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 44 " 0.001 2.00e-02 2.50e+03 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1599 2.75 - 3.29: 16742 3.29 - 3.83: 25708 3.83 - 4.36: 29827 4.36 - 4.90: 51089 Nonbonded interactions: 124965 Sorted by model distance: nonbonded pdb=" OE1 GLN C 66 " pdb=" OG SER C 299 " model vdw 2.213 3.040 nonbonded pdb=" OE1 GLN B 66 " pdb=" OG SER B 299 " model vdw 2.233 3.040 nonbonded pdb=" OE1 GLN D 66 " pdb=" OG SER D 299 " model vdw 2.235 3.040 nonbonded pdb=" OE1 GLN A 66 " pdb=" OG SER A 299 " model vdw 2.237 3.040 nonbonded pdb=" CG2 VAL A 329 " pdb=" OE2 GLU A 520 " model vdw 2.242 3.460 ... (remaining 124960 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: 0.03 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.660 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.004 0.065 16156 Z= 0.223 Angle : 0.853 9.617 21856 Z= 0.467 Chirality : 0.053 0.468 2492 Planarity : 0.004 0.037 2676 Dihedral : 15.597 73.761 5796 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.81 % Favored : 92.98 % Rotamer: Outliers : 0.11 % Allowed : 22.93 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.47 (0.14), residues: 1880 helix: -2.94 (0.11), residues: 1084 sheet: -2.19 (0.23), residues: 260 loop : -2.80 (0.22), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 479 TYR 0.019 0.002 TYR C 426 PHE 0.046 0.003 PHE B 44 TRP 0.010 0.002 TRP C 475 HIS 0.005 0.001 HIS B 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (16148) covalent geometry : angle 0.83191 / 0.46 (21832) hydrogen bonds : bond 0.16065 / 10.82 ( 1026) hydrogen bonds : angle 9.62702 / 6.77 ( 3078) link_NAG-ASN : bond 0.01689 / 0.81 ( 8) link_NAG-ASN : angle 5.74011 / 3.68 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 498 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8412 (tpt170) cc_final: 0.7886 (ttm110) REVERT: A 58 ARG cc_start: 0.6961 (ttt90) cc_final: 0.6115 (tpt170) REVERT: A 61 TRP cc_start: 0.7531 (m100) cc_final: 0.7231 (m100) REVERT: A 164 LYS cc_start: 0.8391 (tttt) cc_final: 0.5549 (ttpt) REVERT: A 165 ARG cc_start: 0.7834 (ttp-110) cc_final: 0.7175 (ttp80) REVERT: A 180 GLU cc_start: 0.8180 (tt0) cc_final: 0.7358 (mm-30) REVERT: A 289 ASP cc_start: 0.8529 (m-30) cc_final: 0.7966 (m-30) REVERT: A 298 VAL cc_start: 0.8350 (t) cc_final: 0.8081 (t) REVERT: A 307 VAL cc_start: 0.9346 (t) cc_final: 0.9121 (t) REVERT: A 314 GLN cc_start: 0.8938 (pt0) cc_final: 0.8513 (tm-30) REVERT: A 335 MET cc_start: 0.8506 (mmm) cc_final: 0.8195 (mmp) REVERT: A 337 PHE cc_start: 0.8205 (m-80) cc_final: 0.7362 (m-80) REVERT: A 344 MET cc_start: 0.8642 (ttm) cc_final: 0.8415 (ttm) REVERT: A 345 ILE cc_start: 0.9277 (mm) cc_final: 0.8966 (mm) REVERT: A 460 MET cc_start: 0.9074 (ttm) cc_final: 0.8785 (ttm) REVERT: A 470 LYS cc_start: 0.8673 (tttt) cc_final: 0.8461 (mmtt) REVERT: A 503 ASP cc_start: 0.8366 (t70) cc_final: 0.7846 (m-30) REVERT: A 522 ARG cc_start: 0.7689 (tpt170) cc_final: 0.7356 (ttm110) REVERT: B 40 ARG cc_start: 0.8305 (tpt170) cc_final: 0.7781 (ttm110) REVERT: B 58 ARG cc_start: 0.6949 (ttt90) cc_final: 0.6555 (tpt170) REVERT: B 61 TRP cc_start: 0.7523 (m100) cc_final: 0.7249 (m-10) REVERT: B 165 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7086 (ttp80) REVERT: B 180 GLU cc_start: 0.8136 (tt0) cc_final: 0.7350 (mm-30) REVERT: B 208 LEU cc_start: 0.8580 (mp) cc_final: 0.8310 (mt) REVERT: B 244 THR cc_start: 0.8870 (p) cc_final: 0.7587 (m) REVERT: B 261 ASP cc_start: 0.8634 (m-30) cc_final: 0.8417 (p0) REVERT: B 266 ILE cc_start: 0.9114 (mt) cc_final: 0.8866 (mp) REVERT: B 298 VAL cc_start: 0.8404 (t) cc_final: 0.8123 (t) REVERT: B 307 VAL cc_start: 0.9261 (t) cc_final: 0.9060 (t) REVERT: B 311 LEU cc_start: 0.8987 (mt) cc_final: 0.8617 (tp) REVERT: B 314 GLN cc_start: 0.8804 (pt0) cc_final: 0.8280 (tm-30) REVERT: B 335 MET cc_start: 0.8498 (mmm) cc_final: 0.8185 (mmp) REVERT: B 337 PHE cc_start: 0.8280 (m-80) cc_final: 0.7425 (m-80) REVERT: B 345 ILE cc_start: 0.9199 (mm) cc_final: 0.8942 (mm) REVERT: B 385 TRP cc_start: 0.9280 (m100) cc_final: 0.8996 (m100) REVERT: B 421 MET cc_start: 0.9319 (mmp) cc_final: 0.9010 (mmm) REVERT: B 460 MET cc_start: 0.9103 (ttm) cc_final: 0.8789 (ttm) REVERT: B 479 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.7921 (ttm170) REVERT: B 503 ASP cc_start: 0.8316 (t70) cc_final: 0.7785 (m-30) REVERT: B 513 GLN cc_start: 0.8557 (tt0) cc_final: 0.8313 (mt0) REVERT: C 164 LYS cc_start: 0.8339 (tttt) cc_final: 0.5345 (ttpt) REVERT: C 165 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7361 (ttp80) REVERT: C 180 GLU cc_start: 0.8245 (tt0) cc_final: 0.7573 (mm-30) REVERT: C 266 ILE cc_start: 0.9096 (mt) cc_final: 0.8859 (mp) REVERT: C 286 MET cc_start: 0.9013 (mmm) cc_final: 0.8771 (tpp) REVERT: C 298 VAL cc_start: 0.8721 (t) cc_final: 0.8463 (t) REVERT: C 314 GLN cc_start: 0.9046 (pt0) cc_final: 0.8471 (tm-30) REVERT: C 317 PHE cc_start: 0.8398 (t80) cc_final: 0.7929 (t80) REVERT: C 335 MET cc_start: 0.8431 (mmm) cc_final: 0.8175 (mmp) REVERT: C 337 PHE cc_start: 0.7963 (m-80) cc_final: 0.7320 (m-80) REVERT: C 345 ILE cc_start: 0.9199 (mm) cc_final: 0.8798 (mm) REVERT: C 421 MET cc_start: 0.9381 (mmp) cc_final: 0.9134 (mmm) REVERT: C 460 MET cc_start: 0.8940 (ttm) cc_final: 0.8256 (ttm) REVERT: C 470 LYS cc_start: 0.9026 (tttt) cc_final: 0.8817 (mmtt) REVERT: C 479 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8256 (tpp80) REVERT: C 503 ASP cc_start: 0.8272 (t70) cc_final: 0.8008 (m-30) REVERT: C 511 TYR cc_start: 0.7997 (m-10) cc_final: 0.7796 (m-10) REVERT: D 50 CYS cc_start: 0.7091 (m) cc_final: 0.6781 (t) REVERT: D 126 LEU cc_start: 0.9181 (mt) cc_final: 0.8957 (tp) REVERT: D 164 LYS cc_start: 0.8341 (tttt) cc_final: 0.4822 (ttpt) REVERT: D 165 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7274 (ttp80) REVERT: D 180 GLU cc_start: 0.8248 (tt0) cc_final: 0.7359 (mm-30) REVERT: D 266 ILE cc_start: 0.9027 (mt) cc_final: 0.8734 (mp) REVERT: D 289 ASP cc_start: 0.8661 (m-30) cc_final: 0.8065 (m-30) REVERT: D 298 VAL cc_start: 0.8503 (t) cc_final: 0.8254 (t) REVERT: D 314 GLN cc_start: 0.8977 (pt0) cc_final: 0.8475 (tm-30) REVERT: D 317 PHE cc_start: 0.8213 (t80) cc_final: 0.7668 (t80) REVERT: D 337 PHE cc_start: 0.7856 (m-80) cc_final: 0.7123 (m-80) REVERT: D 344 MET cc_start: 0.8750 (ttm) cc_final: 0.8535 (ttm) REVERT: D 345 ILE cc_start: 0.9187 (mm) cc_final: 0.8765 (mm) REVERT: D 460 MET cc_start: 0.8813 (ttm) cc_final: 0.8153 (mtt) REVERT: D 467 MET cc_start: 0.9201 (mmm) cc_final: 0.8725 (mmm) REVERT: D 503 ASP cc_start: 0.8279 (t70) cc_final: 0.7993 (m-30) outliers start: 2 outliers final: 0 residues processed: 500 average time/residue: 0.1328 time to fit residues: 98.7369 Evaluate side-chains 331 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 329 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 479 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0050 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN A 339 ASN A 445 ASN B 339 ASN B 445 ASN C 339 ASN D 281 ASN D 339 ASN D 445 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.165726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.115839 restraints weight = 22385.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.119778 restraints weight = 11522.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122218 restraints weight = 7958.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.123198 restraints weight = 6565.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123854 restraints weight = 6002.727| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16156 Z= 0.144 Angle : 0.646 9.714 21856 Z= 0.344 Chirality : 0.043 0.229 2492 Planarity : 0.004 0.041 2676 Dihedral : 5.669 42.124 2068 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.23 % Allowed : 21.61 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.18), residues: 1880 helix: 0.03 (0.14), residues: 1116 sheet: -1.29 (0.28), residues: 248 loop : -1.85 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 479 TYR 0.012 0.001 TYR A 481 PHE 0.024 0.002 PHE A 497 TRP 0.012 0.001 TRP A 475 HIS 0.005 0.001 HIS B 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (16148) covalent geometry : angle 0.62468 / 0.34 (21832) hydrogen bonds : bond 0.05336 / 3.54 ( 1026) hydrogen bonds : angle 5.35031 / 3.83 ( 3078) link_NAG-ASN : bond 0.01074 / 0.50 ( 8) link_NAG-ASN : angle 5.06401 / 3.47 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 358 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.6293 (mt-10) cc_final: 0.5404 (mt-10) REVERT: A 174 THR cc_start: 0.7515 (p) cc_final: 0.7263 (t) REVERT: A 181 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8608 (mp) REVERT: A 232 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6861 (m90) REVERT: A 240 ASP cc_start: 0.7201 (t0) cc_final: 0.6517 (t0) REVERT: A 298 VAL cc_start: 0.8562 (t) cc_final: 0.8202 (t) REVERT: A 317 PHE cc_start: 0.7974 (t80) cc_final: 0.7630 (t80) REVERT: A 335 MET cc_start: 0.7883 (mmm) cc_final: 0.7598 (mmp) REVERT: A 344 MET cc_start: 0.8204 (ttm) cc_final: 0.7895 (ttm) REVERT: A 345 ILE cc_start: 0.8778 (mm) cc_final: 0.7973 (mm) REVERT: A 460 MET cc_start: 0.8070 (ttm) cc_final: 0.7851 (mtm) REVERT: B 156 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7399 (ttt) REVERT: B 232 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.7130 (m90) REVERT: B 317 PHE cc_start: 0.8365 (t80) cc_final: 0.8018 (t80) REVERT: B 335 MET cc_start: 0.7795 (mmm) cc_final: 0.7495 (mmp) REVERT: B 341 TRP cc_start: 0.8147 (m100) cc_final: 0.7245 (m100) REVERT: B 345 ILE cc_start: 0.8841 (mm) cc_final: 0.8237 (mm) REVERT: B 421 MET cc_start: 0.8692 (mmp) cc_final: 0.8452 (mmm) REVERT: B 460 MET cc_start: 0.8438 (ttm) cc_final: 0.8169 (ttp) REVERT: B 479 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7975 (mmt-90) REVERT: B 513 GLN cc_start: 0.8374 (tt0) cc_final: 0.7613 (tm-30) REVERT: C 47 MET cc_start: 0.6776 (tpt) cc_final: 0.6548 (tpp) REVERT: C 56 ARG cc_start: 0.7649 (ttt-90) cc_final: 0.7200 (ttp80) REVERT: C 61 TRP cc_start: 0.6544 (m100) cc_final: 0.5989 (m-10) REVERT: C 72 MET cc_start: 0.8615 (mmt) cc_final: 0.8408 (mmp) REVERT: C 156 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7350 (ttt) REVERT: C 232 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6961 (m90) REVERT: C 279 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7845 (tp-100) REVERT: C 298 VAL cc_start: 0.8735 (t) cc_final: 0.8303 (t) REVERT: C 317 PHE cc_start: 0.8130 (t80) cc_final: 0.7733 (t80) REVERT: C 319 ASN cc_start: 0.8444 (m110) cc_final: 0.8066 (p0) REVERT: C 335 MET cc_start: 0.7923 (mmm) cc_final: 0.7532 (mmp) REVERT: C 402 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8815 (tt) REVERT: C 421 MET cc_start: 0.8775 (mmp) cc_final: 0.8556 (mmm) REVERT: C 479 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7797 (mmt-90) REVERT: D 47 MET cc_start: 0.6141 (tpt) cc_final: 0.5936 (tpp) REVERT: D 72 MET cc_start: 0.8561 (mmt) cc_final: 0.8357 (mmp) REVERT: D 126 LEU cc_start: 0.9046 (mt) cc_final: 0.8723 (tt) REVERT: D 147 GLU cc_start: 0.6497 (mt-10) cc_final: 0.5610 (mt-10) REVERT: D 232 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6957 (m-70) REVERT: D 240 ASP cc_start: 0.7296 (t0) cc_final: 0.6664 (t0) REVERT: D 317 PHE cc_start: 0.8026 (t80) cc_final: 0.7504 (t80) REVERT: D 319 ASN cc_start: 0.8488 (m110) cc_final: 0.8086 (p0) REVERT: D 344 MET cc_start: 0.8251 (ttm) cc_final: 0.7942 (ttp) REVERT: D 345 ILE cc_start: 0.8578 (mm) cc_final: 0.7962 (mm) REVERT: D 460 MET cc_start: 0.8329 (ttm) cc_final: 0.8080 (mtm) REVERT: D 479 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8224 (mmt-90) outliers start: 91 outliers final: 37 residues processed: 420 average time/residue: 0.1292 time to fit residues: 81.4592 Evaluate side-chains 334 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 286 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 156 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN C 281 ASN D 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.166565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.123873 restraints weight = 22634.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.124936 restraints weight = 16061.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125708 restraints weight = 17640.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.127029 restraints weight = 11257.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.127373 restraints weight = 9891.951| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16156 Z= 0.129 Angle : 0.572 9.333 21856 Z= 0.304 Chirality : 0.041 0.229 2492 Planarity : 0.003 0.038 2676 Dihedral : 5.105 40.436 2068 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.60 % Allowed : 22.07 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.23 (0.19), residues: 1880 helix: 1.24 (0.15), residues: 1116 sheet: -1.01 (0.29), residues: 248 loop : -1.59 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 231 TYR 0.013 0.001 TYR A 481 PHE 0.018 0.002 PHE A 497 TRP 0.007 0.001 TRP B 272 HIS 0.003 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (16148) covalent geometry : angle 0.55097 / 0.30 (21832) hydrogen bonds : bond 0.04685 / 3.10 ( 1026) hydrogen bonds : angle 4.80022 / 3.45 ( 3078) link_NAG-ASN : bond 0.00953 / 0.44 ( 8) link_NAG-ASN : angle 4.63020 / 3.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 324 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8238 (t80) REVERT: A 147 GLU cc_start: 0.6680 (mt-10) cc_final: 0.5730 (mt-10) REVERT: A 181 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 232 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6786 (m90) REVERT: A 240 ASP cc_start: 0.7364 (t0) cc_final: 0.6861 (t0) REVERT: A 283 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7602 (p90) REVERT: A 315 GLN cc_start: 0.8388 (mm-40) cc_final: 0.8131 (mm-40) REVERT: A 335 MET cc_start: 0.7674 (mmm) cc_final: 0.7206 (mmp) REVERT: A 344 MET cc_start: 0.8031 (ttm) cc_final: 0.7729 (ttm) REVERT: B 156 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7292 (ttt) REVERT: B 226 ASN cc_start: 0.8186 (t0) cc_final: 0.7960 (t0) REVERT: B 232 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.7097 (m90) REVERT: B 283 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7423 (p90) REVERT: B 335 MET cc_start: 0.7568 (mmm) cc_final: 0.7228 (mmp) REVERT: B 479 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7731 (mmt-90) REVERT: C 56 ARG cc_start: 0.7638 (ttt-90) cc_final: 0.7223 (ttp80) REVERT: C 61 TRP cc_start: 0.6356 (m100) cc_final: 0.5802 (m-10) REVERT: C 232 HIS cc_start: 0.7262 (OUTLIER) cc_final: 0.6974 (m90) REVERT: C 279 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7802 (tp-100) REVERT: C 314 GLN cc_start: 0.8370 (tm-30) cc_final: 0.7605 (tm-30) REVERT: C 315 GLN cc_start: 0.8703 (mm110) cc_final: 0.8301 (mm110) REVERT: C 317 PHE cc_start: 0.8068 (t80) cc_final: 0.7777 (t80) REVERT: C 335 MET cc_start: 0.7999 (mmm) cc_final: 0.7713 (mmp) REVERT: C 402 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8547 (pt) REVERT: C 421 MET cc_start: 0.8759 (mmp) cc_final: 0.8475 (mmm) REVERT: C 424 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8413 (tp) REVERT: C 450 CYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7528 (t) REVERT: C 459 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7832 (t0) REVERT: C 479 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7569 (mmt-90) REVERT: D 126 LEU cc_start: 0.9036 (mt) cc_final: 0.8698 (tt) REVERT: D 147 GLU cc_start: 0.6492 (mt-10) cc_final: 0.5695 (mt-10) REVERT: D 232 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6903 (m-70) REVERT: D 240 ASP cc_start: 0.7380 (t0) cc_final: 0.6816 (t0) REVERT: D 315 GLN cc_start: 0.8210 (mm110) cc_final: 0.7555 (mm-40) REVERT: D 317 PHE cc_start: 0.7955 (t80) cc_final: 0.7578 (t80) REVERT: D 319 ASN cc_start: 0.8290 (m110) cc_final: 0.8066 (p0) REVERT: D 421 MET cc_start: 0.8962 (mmp) cc_final: 0.8462 (mmm) REVERT: D 450 CYS cc_start: 0.8143 (OUTLIER) cc_final: 0.7919 (t) REVERT: D 459 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7755 (t0) outliers start: 80 outliers final: 33 residues processed: 380 average time/residue: 0.1173 time to fit residues: 69.3079 Evaluate side-chains 327 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 277 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 492 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 450 CYS Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 459 ASP Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 178 optimal weight: 1.9990 chunk 166 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 151 optimal weight: 0.5980 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN B 76 GLN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN C 281 ASN C 324 HIS D 100 HIS D 125 GLN D 281 ASN D 312 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.117691 restraints weight = 22668.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121983 restraints weight = 17655.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.122217 restraints weight = 14284.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122102 restraints weight = 10196.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122491 restraints weight = 9403.640| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16156 Z= 0.252 Angle : 0.660 11.854 21856 Z= 0.348 Chirality : 0.044 0.232 2492 Planarity : 0.004 0.049 2676 Dihedral : 5.206 40.633 2068 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 6.21 % Allowed : 22.47 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.29 (0.19), residues: 1880 helix: 1.25 (0.15), residues: 1124 sheet: -0.79 (0.29), residues: 280 loop : -1.63 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 390 TYR 0.018 0.002 TYR A 481 PHE 0.024 0.002 PHE A 497 TRP 0.010 0.001 TRP B 272 HIS 0.004 0.001 HIS D 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.25 (16148) covalent geometry : angle 0.63615 / 0.34 (21832) hydrogen bonds : bond 0.05222 / 3.49 ( 1026) hydrogen bonds : angle 4.90115 / 3.53 ( 3078) link_NAG-ASN : bond 0.00899 / 0.41 ( 8) link_NAG-ASN : angle 5.39010 / 3.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 272 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8331 (t80) REVERT: A 147 GLU cc_start: 0.6450 (mt-10) cc_final: 0.5144 (mt-10) REVERT: A 181 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8659 (mp) REVERT: A 232 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6778 (m-70) REVERT: A 283 HIS cc_start: 0.8558 (OUTLIER) cc_final: 0.7634 (p90) REVERT: A 335 MET cc_start: 0.7679 (mmm) cc_final: 0.7390 (mmp) REVERT: A 344 MET cc_start: 0.8075 (ttm) cc_final: 0.7846 (ttm) REVERT: A 392 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7623 (mp) REVERT: A 424 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 450 CYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8435 (t) REVERT: A 467 MET cc_start: 0.8552 (mmm) cc_final: 0.8331 (mmm) REVERT: A 476 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8792 (tt) REVERT: B 156 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7418 (ttt) REVERT: B 232 HIS cc_start: 0.7317 (OUTLIER) cc_final: 0.6920 (m90) REVERT: B 240 ASP cc_start: 0.7665 (t0) cc_final: 0.7379 (t0) REVERT: B 283 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.7483 (p90) REVERT: B 335 MET cc_start: 0.7730 (mmm) cc_final: 0.7380 (mmp) REVERT: B 345 ILE cc_start: 0.8874 (mm) cc_final: 0.8558 (mm) REVERT: B 450 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8495 (t) REVERT: B 476 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 479 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7699 (mmt-90) REVERT: C 56 ARG cc_start: 0.7673 (ttt-90) cc_final: 0.7199 (ttp80) REVERT: C 232 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6913 (m90) REVERT: C 317 PHE cc_start: 0.8090 (t80) cc_final: 0.7852 (t80) REVERT: C 335 MET cc_start: 0.8125 (mmm) cc_final: 0.7837 (mmp) REVERT: C 337 PHE cc_start: 0.8034 (m-80) cc_final: 0.7383 (m-80) REVERT: C 424 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8442 (tp) REVERT: C 450 CYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8474 (t) REVERT: C 476 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8871 (tt) REVERT: C 479 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7398 (mpt180) REVERT: D 147 GLU cc_start: 0.6573 (mt-10) cc_final: 0.5696 (mt-10) REVERT: D 232 HIS cc_start: 0.7110 (OUTLIER) cc_final: 0.6816 (m-70) REVERT: D 240 ASP cc_start: 0.7513 (t0) cc_final: 0.7050 (t0) REVERT: D 315 GLN cc_start: 0.8067 (mm110) cc_final: 0.7678 (mm-40) REVERT: D 317 PHE cc_start: 0.8046 (t80) cc_final: 0.7717 (t80) REVERT: D 421 MET cc_start: 0.8928 (mmp) cc_final: 0.8720 (mmm) REVERT: D 424 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8550 (tp) REVERT: D 450 CYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (t) outliers start: 108 outliers final: 53 residues processed: 355 average time/residue: 0.1175 time to fit residues: 64.6437 Evaluate side-chains 332 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 257 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 450 CYS Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 450 CYS Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 450 CYS Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 504 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 60 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 100 HIS A 281 ASN B 100 HIS C 100 HIS C 281 ASN D 281 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.163798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.116959 restraints weight = 22458.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118190 restraints weight = 12650.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.119401 restraints weight = 9023.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.119656 restraints weight = 8118.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120060 restraints weight = 7565.866| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16156 Z= 0.157 Angle : 0.587 12.128 21856 Z= 0.306 Chirality : 0.041 0.219 2492 Planarity : 0.003 0.040 2676 Dihedral : 5.001 41.114 2068 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.52 % Allowed : 22.76 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.19), residues: 1880 helix: 1.51 (0.15), residues: 1120 sheet: -0.62 (0.29), residues: 280 loop : -1.55 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 231 TYR 0.014 0.001 TYR D 481 PHE 0.020 0.002 PHE B 497 TRP 0.008 0.001 TRP B 272 HIS 0.003 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (16148) covalent geometry : angle 0.55460 / 0.30 (21832) hydrogen bonds : bond 0.04667 / 3.11 ( 1026) hydrogen bonds : angle 4.68488 / 3.38 ( 3078) link_NAG-ASN : bond 0.00905 / 0.41 ( 8) link_NAG-ASN : angle 5.82925 / 4.15 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 274 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8344 (mmp) cc_final: 0.8077 (mmm) REVERT: A 232 HIS cc_start: 0.7097 (OUTLIER) cc_final: 0.6728 (m-70) REVERT: A 283 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.7795 (p90) REVERT: A 292 VAL cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (p) REVERT: A 326 LYS cc_start: 0.8242 (mttt) cc_final: 0.7707 (mtmt) REVERT: A 335 MET cc_start: 0.7749 (mmm) cc_final: 0.7356 (mmp) REVERT: A 344 MET cc_start: 0.8120 (ttm) cc_final: 0.7855 (ttm) REVERT: B 38 MET cc_start: 0.7111 (ppp) cc_final: 0.6616 (ppp) REVERT: B 56 ARG cc_start: 0.7489 (tmm160) cc_final: 0.5950 (ptm-80) REVERT: B 156 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.7475 (ttt) REVERT: B 226 ASN cc_start: 0.8364 (t0) cc_final: 0.8075 (t0) REVERT: B 232 HIS cc_start: 0.7278 (OUTLIER) cc_final: 0.6890 (m90) REVERT: B 283 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.7580 (p90) REVERT: B 335 MET cc_start: 0.7655 (mmm) cc_final: 0.7284 (mmp) REVERT: B 363 GLN cc_start: 0.8384 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 479 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8027 (mmp80) REVERT: B 516 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: C 45 PHE cc_start: 0.7487 (t80) cc_final: 0.7232 (t80) REVERT: C 47 MET cc_start: 0.6519 (tpp) cc_final: 0.6226 (tpp) REVERT: C 56 ARG cc_start: 0.7722 (ttt-90) cc_final: 0.7111 (ttp80) REVERT: C 147 GLU cc_start: 0.6221 (mt-10) cc_final: 0.5767 (mt-10) REVERT: C 232 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6869 (m-70) REVERT: C 240 ASP cc_start: 0.7462 (t0) cc_final: 0.7084 (t0) REVERT: C 317 PHE cc_start: 0.8143 (t80) cc_final: 0.7919 (t80) REVERT: C 335 MET cc_start: 0.8026 (mmm) cc_final: 0.7725 (mmp) REVERT: C 349 ASP cc_start: 0.7626 (m-30) cc_final: 0.7407 (m-30) REVERT: C 424 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 432 ILE cc_start: 0.8807 (tp) cc_final: 0.8595 (tp) REVERT: C 479 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7932 (mmt-90) REVERT: D 72 MET cc_start: 0.8278 (tpp) cc_final: 0.8018 (mmm) REVERT: D 232 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6752 (m-70) REVERT: D 317 PHE cc_start: 0.7852 (t80) cc_final: 0.7551 (t80) REVERT: D 390 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7690 (ttp-170) REVERT: D 421 MET cc_start: 0.8940 (mmp) cc_final: 0.8655 (mmp) REVERT: D 424 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8531 (tp) REVERT: D 476 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9017 (tt) outliers start: 96 outliers final: 57 residues processed: 348 average time/residue: 0.1204 time to fit residues: 64.5298 Evaluate side-chains 326 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 254 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 186 PHE Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 508 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 0.2980 chunk 119 optimal weight: 9.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN C 125 GLN C 281 ASN D 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.162529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.119800 restraints weight = 22461.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119131 restraints weight = 16186.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121038 restraints weight = 13856.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.121729 restraints weight = 10815.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122385 restraints weight = 10441.165| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16156 Z= 0.191 Angle : 0.610 12.149 21856 Z= 0.317 Chirality : 0.041 0.212 2492 Planarity : 0.003 0.040 2676 Dihedral : 4.974 42.625 2068 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 6.03 % Allowed : 22.82 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.19), residues: 1880 helix: 1.63 (0.15), residues: 1112 sheet: -0.72 (0.28), residues: 276 loop : -1.59 (0.25), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 231 TYR 0.016 0.002 TYR D 481 PHE 0.020 0.002 PHE B 497 TRP 0.009 0.001 TRP B 272 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (16148) covalent geometry : angle 0.57987 / 0.31 (21832) hydrogen bonds : bond 0.04684 / 3.13 ( 1026) hydrogen bonds : angle 4.68092 / 3.38 ( 3078) link_NAG-ASN : bond 0.00940 / 0.42 ( 8) link_NAG-ASN : angle 5.70805 / 4.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 264 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6194 (tpp) cc_final: 0.5931 (tpp) REVERT: A 72 MET cc_start: 0.8394 (mmp) cc_final: 0.8122 (mmm) REVERT: A 232 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6719 (m-70) REVERT: A 283 HIS cc_start: 0.8567 (OUTLIER) cc_final: 0.7652 (p90) REVERT: A 292 VAL cc_start: 0.9044 (OUTLIER) cc_final: 0.8817 (p) REVERT: A 326 LYS cc_start: 0.8164 (mttt) cc_final: 0.7619 (mtmt) REVERT: A 335 MET cc_start: 0.7872 (mmm) cc_final: 0.7478 (mmp) REVERT: A 344 MET cc_start: 0.8113 (ttm) cc_final: 0.7873 (ttm) REVERT: A 450 CYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8208 (t) REVERT: B 38 MET cc_start: 0.6890 (ppp) cc_final: 0.6511 (ppp) REVERT: B 47 MET cc_start: 0.6417 (tpp) cc_final: 0.6138 (tpp) REVERT: B 156 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7315 (ttt) REVERT: B 226 ASN cc_start: 0.8415 (t0) cc_final: 0.8122 (t0) REVERT: B 232 HIS cc_start: 0.7219 (OUTLIER) cc_final: 0.6832 (m90) REVERT: B 283 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.7504 (p90) REVERT: B 335 MET cc_start: 0.7732 (mmm) cc_final: 0.7363 (mmp) REVERT: B 363 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 476 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8962 (tt) REVERT: B 479 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7503 (mpt180) REVERT: B 516 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: C 45 PHE cc_start: 0.7596 (t80) cc_final: 0.7385 (t80) REVERT: C 232 HIS cc_start: 0.7130 (OUTLIER) cc_final: 0.6781 (m-70) REVERT: C 317 PHE cc_start: 0.8101 (t80) cc_final: 0.7865 (t80) REVERT: C 335 MET cc_start: 0.7813 (mmm) cc_final: 0.7494 (mmp) REVERT: C 390 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7989 (ttp-170) REVERT: C 424 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8375 (tp) REVERT: C 476 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8956 (tt) REVERT: C 479 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7826 (mmt-90) REVERT: D 147 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6331 (mt-10) REVERT: D 232 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6762 (m-70) REVERT: D 240 ASP cc_start: 0.7491 (t0) cc_final: 0.7169 (t0) REVERT: D 421 MET cc_start: 0.8895 (mmp) cc_final: 0.8651 (mmp) REVERT: D 424 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8399 (tp) REVERT: D 476 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8984 (tt) outliers start: 105 outliers final: 75 residues processed: 344 average time/residue: 0.1153 time to fit residues: 61.7837 Evaluate side-chains 349 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 256 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain B residue 508 ILE Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 494 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 508 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 44 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 184 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 168 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN C 273 HIS C 281 ASN D 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.165581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116606 restraints weight = 22319.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120361 restraints weight = 11840.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.122696 restraints weight = 8263.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123829 restraints weight = 6819.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124205 restraints weight = 6194.958| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16156 Z= 0.134 Angle : 0.579 11.919 21856 Z= 0.297 Chirality : 0.040 0.223 2492 Planarity : 0.003 0.042 2676 Dihedral : 4.837 42.395 2068 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 5.00 % Allowed : 23.56 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.19), residues: 1880 helix: 1.83 (0.15), residues: 1112 sheet: -0.61 (0.29), residues: 276 loop : -1.53 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.014 0.001 TYR A 481 PHE 0.017 0.001 PHE B 497 TRP 0.010 0.001 TRP C 272 HIS 0.002 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16148) covalent geometry : angle 0.54975 / 0.29 (21832) hydrogen bonds : bond 0.04354 / 2.92 ( 1026) hydrogen bonds : angle 4.54502 / 3.28 ( 3078) link_NAG-ASN : bond 0.00913 / 0.40 ( 8) link_NAG-ASN : angle 5.54135 / 3.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 273 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.5984 (p90) REVERT: A 72 MET cc_start: 0.8281 (mmp) cc_final: 0.8044 (mmm) REVERT: A 232 HIS cc_start: 0.7086 (OUTLIER) cc_final: 0.6731 (m-70) REVERT: A 283 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.7618 (p90) REVERT: A 292 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 335 MET cc_start: 0.7822 (mmm) cc_final: 0.7432 (mmp) REVERT: A 344 MET cc_start: 0.8085 (ttm) cc_final: 0.7877 (ttm) REVERT: A 424 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8551 (tp) REVERT: B 38 MET cc_start: 0.7079 (ppp) cc_final: 0.6647 (ppp) REVERT: B 44 PHE cc_start: 0.6801 (OUTLIER) cc_final: 0.5639 (p90) REVERT: B 56 ARG cc_start: 0.7527 (tmm160) cc_final: 0.5773 (ptm-80) REVERT: B 226 ASN cc_start: 0.8448 (t0) cc_final: 0.8136 (t0) REVERT: B 232 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6825 (m-70) REVERT: B 283 HIS cc_start: 0.8393 (OUTLIER) cc_final: 0.7422 (p90) REVERT: B 335 MET cc_start: 0.7686 (mmm) cc_final: 0.7302 (mmp) REVERT: B 363 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 476 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8925 (tt) REVERT: B 479 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7584 (mpt180) REVERT: B 516 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6947 (m-80) REVERT: C 232 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6637 (m90) REVERT: C 335 MET cc_start: 0.7741 (mmm) cc_final: 0.7418 (mmp) REVERT: C 390 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7911 (ttp-170) REVERT: C 424 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8389 (tp) REVERT: C 479 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7889 (mmt-90) REVERT: D 38 MET cc_start: 0.7657 (tmm) cc_final: 0.7102 (tmm) REVERT: D 45 PHE cc_start: 0.7455 (t80) cc_final: 0.7240 (t80) REVERT: D 147 GLU cc_start: 0.6442 (mt-10) cc_final: 0.6123 (mt-10) REVERT: D 232 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6680 (m-70) REVERT: D 240 ASP cc_start: 0.7368 (t0) cc_final: 0.7010 (t0) REVERT: D 272 TRP cc_start: 0.7346 (t60) cc_final: 0.6997 (t60) REVERT: D 281 ASN cc_start: 0.6264 (OUTLIER) cc_final: 0.5818 (m-40) REVERT: D 390 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7956 (ttp-110) REVERT: D 424 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8426 (tp) REVERT: D 476 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8969 (tt) outliers start: 87 outliers final: 49 residues processed: 338 average time/residue: 0.1218 time to fit residues: 63.9368 Evaluate side-chains 336 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 267 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 186 PHE Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 142 optimal weight: 0.0570 chunk 176 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN C 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.168533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126065 restraints weight = 22364.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.126084 restraints weight = 14437.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127578 restraints weight = 12511.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128012 restraints weight = 10047.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128625 restraints weight = 9617.779| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16156 Z= 0.114 Angle : 0.574 12.327 21856 Z= 0.289 Chirality : 0.040 0.174 2492 Planarity : 0.003 0.043 2676 Dihedral : 4.687 41.150 2068 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.25 % Allowed : 24.66 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.19), residues: 1880 helix: 2.03 (0.15), residues: 1112 sheet: -0.43 (0.30), residues: 268 loop : -1.52 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.014 0.001 TYR A 481 PHE 0.015 0.001 PHE B 497 TRP 0.010 0.001 TRP A 475 HIS 0.002 0.001 HIS C 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16148) covalent geometry : angle 0.54363 / 0.28 (21832) hydrogen bonds : bond 0.04026 / 2.70 ( 1026) hydrogen bonds : angle 4.43289 / 3.20 ( 3078) link_NAG-ASN : bond 0.00915 / 0.39 ( 8) link_NAG-ASN : angle 5.55649 / 3.82 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 289 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.5952 (p90) REVERT: A 232 HIS cc_start: 0.7129 (OUTLIER) cc_final: 0.6743 (m90) REVERT: A 283 HIS cc_start: 0.8599 (OUTLIER) cc_final: 0.7698 (p90) REVERT: A 335 MET cc_start: 0.7767 (mmm) cc_final: 0.7379 (mmp) REVERT: A 424 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8473 (tp) REVERT: B 38 MET cc_start: 0.6852 (ppp) cc_final: 0.6557 (ppp) REVERT: B 44 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5682 (p90) REVERT: B 47 MET cc_start: 0.6387 (tpp) cc_final: 0.6184 (tpp) REVERT: B 56 ARG cc_start: 0.7472 (tmm160) cc_final: 0.5691 (ptm-80) REVERT: B 226 ASN cc_start: 0.8382 (t0) cc_final: 0.8031 (t0) REVERT: B 232 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6697 (m90) REVERT: B 283 HIS cc_start: 0.8365 (OUTLIER) cc_final: 0.7398 (p90) REVERT: B 335 MET cc_start: 0.7686 (mmm) cc_final: 0.7321 (mmp) REVERT: B 479 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7647 (mmt-90) REVERT: B 516 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: C 38 MET cc_start: 0.7163 (OUTLIER) cc_final: 0.6915 (tmm) REVERT: C 47 MET cc_start: 0.6619 (tpp) cc_final: 0.6419 (tpp) REVERT: C 232 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6583 (m-70) REVERT: C 335 MET cc_start: 0.7696 (mmm) cc_final: 0.7259 (mmp) REVERT: C 390 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7974 (ttp-110) REVERT: C 424 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8146 (tp) REVERT: C 479 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7582 (mmt-90) REVERT: D 38 MET cc_start: 0.7308 (tmm) cc_final: 0.7004 (tmm) REVERT: D 232 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6620 (m-70) REVERT: D 240 ASP cc_start: 0.7413 (t0) cc_final: 0.6944 (t70) REVERT: D 272 TRP cc_start: 0.7193 (t60) cc_final: 0.6936 (t60) REVERT: D 281 ASN cc_start: 0.6415 (OUTLIER) cc_final: 0.5725 (m-40) REVERT: D 390 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7882 (ttp-170) REVERT: D 421 MET cc_start: 0.8783 (mmp) cc_final: 0.8336 (mmm) REVERT: D 424 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8317 (tp) REVERT: D 476 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8890 (tt) outliers start: 74 outliers final: 45 residues processed: 340 average time/residue: 0.1171 time to fit residues: 61.9425 Evaluate side-chains 326 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 283 HIS Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 489 PHE Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Chi-restraints excluded: chain D residue 487 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN A 456 ASN C 281 ASN C 456 ASN D 281 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126129 restraints weight = 22397.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126677 restraints weight = 14191.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.127933 restraints weight = 12094.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.128238 restraints weight = 9690.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.131108 restraints weight = 9304.677| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16156 Z= 0.116 Angle : 0.571 11.966 21856 Z= 0.286 Chirality : 0.040 0.184 2492 Planarity : 0.003 0.042 2676 Dihedral : 4.596 40.584 2068 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.91 % Allowed : 25.75 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.19), residues: 1880 helix: 2.03 (0.15), residues: 1136 sheet: -0.28 (0.31), residues: 268 loop : -1.36 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.015 0.001 TYR A 481 PHE 0.018 0.001 PHE A 317 TRP 0.010 0.001 TRP A 475 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (16148) covalent geometry : angle 0.54367 / 0.28 (21832) hydrogen bonds : bond 0.03953 / 2.65 ( 1026) hydrogen bonds : angle 4.38556 / 3.16 ( 3078) link_NAG-ASN : bond 0.00868 / 0.36 ( 8) link_NAG-ASN : angle 5.30986 / 3.64 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 284 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 232 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6796 (m-70) REVERT: A 283 HIS cc_start: 0.8495 (OUTLIER) cc_final: 0.7569 (p90) REVERT: A 335 MET cc_start: 0.7704 (mmm) cc_final: 0.7337 (mmp) REVERT: B 38 MET cc_start: 0.6823 (ppp) cc_final: 0.6546 (ppp) REVERT: B 44 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.5641 (p90) REVERT: B 47 MET cc_start: 0.6458 (tpp) cc_final: 0.6222 (tpp) REVERT: B 56 ARG cc_start: 0.7277 (tmm160) cc_final: 0.5705 (ptm-80) REVERT: B 226 ASN cc_start: 0.8370 (t0) cc_final: 0.8093 (t0) REVERT: B 232 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6664 (m90) REVERT: B 283 HIS cc_start: 0.8370 (OUTLIER) cc_final: 0.7418 (p90) REVERT: B 335 MET cc_start: 0.7682 (mmm) cc_final: 0.7304 (mmp) REVERT: B 421 MET cc_start: 0.8500 (mmp) cc_final: 0.8174 (mmm) REVERT: B 479 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7565 (mmt-90) REVERT: B 516 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: C 38 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6909 (tmm) REVERT: C 44 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.5934 (p90) REVERT: C 232 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.6596 (m-70) REVERT: C 281 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.5927 (m110) REVERT: C 335 MET cc_start: 0.7751 (mmm) cc_final: 0.7322 (mmp) REVERT: C 390 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7947 (ttp-110) REVERT: C 424 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8139 (tp) REVERT: D 38 MET cc_start: 0.7290 (tmm) cc_final: 0.6987 (tmm) REVERT: D 44 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.5944 (p90) REVERT: D 147 GLU cc_start: 0.6667 (mt-10) cc_final: 0.6440 (mt-10) REVERT: D 232 HIS cc_start: 0.6904 (OUTLIER) cc_final: 0.6636 (m-70) REVERT: D 240 ASP cc_start: 0.7246 (t0) cc_final: 0.6967 (t0) REVERT: D 390 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7807 (ttp-170) REVERT: D 421 MET cc_start: 0.8744 (mmp) cc_final: 0.8315 (mmm) REVERT: D 424 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8294 (tp) REVERT: D 476 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8854 (tt) outliers start: 68 outliers final: 46 residues processed: 328 average time/residue: 0.1179 time to fit residues: 60.0878 Evaluate side-chains 331 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 110 MET Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 281 ASN Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 150 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN C 281 ASN D 281 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.168134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124937 restraints weight = 22269.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.126115 restraints weight = 14050.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.127284 restraints weight = 11611.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128105 restraints weight = 9379.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128412 restraints weight = 8878.676| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16156 Z= 0.128 Angle : 0.582 11.893 21856 Z= 0.291 Chirality : 0.040 0.182 2492 Planarity : 0.003 0.041 2676 Dihedral : 4.433 40.999 2064 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Rotamer: Outliers : 3.62 % Allowed : 26.38 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.19), residues: 1880 helix: 2.03 (0.15), residues: 1136 sheet: -0.22 (0.31), residues: 268 loop : -1.32 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.016 0.001 TYR A 481 PHE 0.018 0.001 PHE C 46 TRP 0.013 0.001 TRP C 475 HIS 0.002 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16148) covalent geometry : angle 0.55615 / 0.29 (21832) hydrogen bonds : bond 0.03978 / 2.67 ( 1026) hydrogen bonds : angle 4.37685 / 3.16 ( 3078) link_NAG-ASN : bond 0.00834 / 0.34 ( 8) link_NAG-ASN : angle 5.20444 / 3.55 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6926 (OUTLIER) cc_final: 0.6042 (p90) REVERT: A 232 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6786 (m-70) REVERT: A 283 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7793 (p90) REVERT: A 286 MET cc_start: 0.8739 (mmm) cc_final: 0.8354 (tpp) REVERT: A 335 MET cc_start: 0.7706 (mmm) cc_final: 0.7339 (mmp) REVERT: A 460 MET cc_start: 0.8247 (ttm) cc_final: 0.8006 (mtt) REVERT: B 38 MET cc_start: 0.6833 (ppp) cc_final: 0.6559 (ppp) REVERT: B 44 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5662 (p90) REVERT: B 47 MET cc_start: 0.6699 (tpp) cc_final: 0.6481 (tpp) REVERT: B 56 ARG cc_start: 0.7259 (tmm160) cc_final: 0.5693 (ptm-80) REVERT: B 226 ASN cc_start: 0.8380 (t0) cc_final: 0.8085 (t0) REVERT: B 232 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6618 (m90) REVERT: B 283 HIS cc_start: 0.8408 (OUTLIER) cc_final: 0.7455 (p90) REVERT: B 335 MET cc_start: 0.7682 (mmm) cc_final: 0.7305 (mmp) REVERT: B 479 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7558 (mmt-90) REVERT: B 516 PHE cc_start: 0.7506 (OUTLIER) cc_final: 0.7148 (m-80) REVERT: C 38 MET cc_start: 0.7158 (ppp) cc_final: 0.6931 (tmm) REVERT: C 44 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.5902 (p90) REVERT: C 232 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6568 (m90) REVERT: C 281 ASN cc_start: 0.6592 (OUTLIER) cc_final: 0.6128 (m110) REVERT: C 335 MET cc_start: 0.7753 (mmm) cc_final: 0.7320 (mmp) REVERT: C 390 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7894 (ttp-110) REVERT: C 424 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8177 (tp) REVERT: D 38 MET cc_start: 0.7309 (tmm) cc_final: 0.7003 (tmm) REVERT: D 44 PHE cc_start: 0.6746 (OUTLIER) cc_final: 0.5964 (p90) REVERT: D 147 GLU cc_start: 0.6695 (mt-10) cc_final: 0.6471 (mt-10) REVERT: D 232 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6650 (m-70) REVERT: D 240 ASP cc_start: 0.7261 (t0) cc_final: 0.6996 (t0) REVERT: D 390 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7806 (ttp-170) REVERT: D 421 MET cc_start: 0.8760 (mmp) cc_final: 0.8336 (mmm) REVERT: D 424 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8289 (tp) REVERT: D 476 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8878 (tt) outliers start: 63 outliers final: 43 residues processed: 317 average time/residue: 0.1168 time to fit residues: 57.8235 Evaluate side-chains 324 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 232 HIS Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 291 PHE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 373 CYS Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 110 MET Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 186 PHE Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 281 ASN Chi-restraints excluded: chain B residue 283 HIS Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 373 CYS Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 232 HIS Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 373 CYS Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 426 TYR Chi-restraints excluded: chain C residue 446 MET Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 232 HIS Chi-restraints excluded: chain D residue 246 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 373 CYS Chi-restraints excluded: chain D residue 390 ARG Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 412 VAL Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 30 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN B 456 ASN C 281 ASN D 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.166731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123515 restraints weight = 22321.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123353 restraints weight = 14679.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125070 restraints weight = 12578.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125526 restraints weight = 10016.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.126099 restraints weight = 9682.935| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16156 Z= 0.144 Angle : 0.594 11.820 21856 Z= 0.297 Chirality : 0.040 0.176 2492 Planarity : 0.003 0.040 2676 Dihedral : 4.457 42.047 2064 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.07 % Favored : 97.87 % Rotamer: Outliers : 4.02 % Allowed : 26.44 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.19), residues: 1880 helix: 2.01 (0.15), residues: 1136 sheet: -0.21 (0.31), residues: 268 loop : -1.29 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 479 TYR 0.016 0.001 TYR A 481 PHE 0.017 0.001 PHE A 317 TRP 0.013 0.001 TRP C 272 HIS 0.003 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16148) covalent geometry : angle 0.56924 / 0.29 (21832) hydrogen bonds : bond 0.04082 / 2.74 ( 1026) hydrogen bonds : angle 4.41099 / 3.18 ( 3078) link_NAG-ASN : bond 0.00782 / 0.32 ( 8) link_NAG-ASN : angle 5.10850 / 3.47 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2625.42 seconds wall clock time: 46 minutes 30.56 seconds (2790.56 seconds total)