Starting phenix.real_space_refine on Tue Nov 18 16:43:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ayf_7019/11_2025/6ayf_7019.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ayf_7019/11_2025/6ayf_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ayf_7019/11_2025/6ayf_7019.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ayf_7019/11_2025/6ayf_7019.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ayf_7019/11_2025/6ayf_7019.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ayf_7019/11_2025/6ayf_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.31, per 1000 atoms: 0.27 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: 1.48 Conformation dependent library (CDL) restraints added in 760.2 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: 0.51 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: 3.06 Time building geometry restraints manager: 1.96 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: 8052 14.75 - 29.50: 1121 29.50 - 44.26: 342 44.26 - 59.01: 85 59.01 - 73.76: 20 Dihedral angle restraints: 9620 sinusoidal: 3972 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 9617 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.950 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 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 : 15.595 73.761 5964 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 covalent geometry : bond 0.00440 (16148) covalent geometry : angle 0.83191 (21832) hydrogen bonds : bond 0.16065 ( 1026) hydrogen bonds : angle 9.62702 ( 3078) link_NAG-ASN : bond 0.01689 ( 8) link_NAG-ASN : angle 5.74011 ( 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 : 0.614 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: 0.6116 (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: 0.8365 (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: 0.8137 (tt0) cc_final: 0.7350 (mm-30) REVERT: B 208 LEU cc_start: 0.8580 (mp) cc_final: 0.8309 (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: 0.8803 (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: 0.9009 (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: 0.8009 (m-30) REVERT: C 511 TYR cc_start: 0.7997 (m-10) cc_final: 0.7796 (m-10) REVERT: D 50 CYS cc_start: 0.7090 (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: 0.4823 (ttpt) REVERT: D 165 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7275 (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: 0.7667 (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: 0.8726 (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: 0.1342 time to fit residues: 98.8038 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 : 0.630 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 339 ASN B 339 ASN C 339 ASN D 281 ASN D 339 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.115807 restraints weight = 22307.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.119575 restraints weight = 11810.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.121920 restraints weight = 8291.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123015 restraints weight = 6878.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123015 restraints weight = 6273.583| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2981 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= 0.147 Angle : 0.645 9.851 21856 Z= 0.345 Chirality : 0.043 0.255 2492 Planarity : 0.004 0.040 2676 Dihedral : 6.156 43.011 2236 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.11 % Allowed : 21.44 % Favored : 73.45 % 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: -1.16 (0.18), residues: 1880 helix: -0.05 (0.14), residues: 1116 sheet: -1.27 (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 0.011 0.001 TRP A 475 HIS 0.005 0.001 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00295 (16148) covalent geometry : angle 0.62437 (21832) hydrogen bonds : bond 0.05479 ( 1026) hydrogen bonds : angle 5.44508 ( 3078) link_NAG-ASN : bond 0.01273 ( 8) link_NAG-ASN : angle 4.97521 ( 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 440 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 351 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLU cc_start: 0.6488 (mt-10) cc_final: 0.5575 (mt-10) REVERT: A 174 THR cc_start: 0.7430 (p) cc_final: 0.7178 (t) REVERT: A 181 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 232 HIS cc_start: 0.7164 (OUTLIER) cc_final: 0.6897 (m90) REVERT: A 240 ASP cc_start: 0.7268 (t0) cc_final: 0.6601 (t0) REVERT: A 298 VAL cc_start: 0.8473 (t) cc_final: 0.8065 (t) REVERT: A 317 PHE cc_start: 0.8035 (t80) cc_final: 0.7620 (t80) REVERT: A 335 MET cc_start: 0.7897 (mmm) cc_final: 0.7609 (mmp) REVERT: A 344 MET cc_start: 0.8158 (ttm) cc_final: 0.7830 (ttm) REVERT: A 345 ILE cc_start: 0.8849 (mm) cc_final: 0.8091 (mm) REVERT: A 460 MET cc_start: 0.8084 (ttm) cc_final: 0.7855 (mtm) REVERT: B 156 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7399 (ttt) REVERT: B 232 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7137 (m90) REVERT: B 317 PHE cc_start: 0.8323 (t80) cc_final: 0.7927 (t80) REVERT: B 335 MET cc_start: 0.7815 (mmm) cc_final: 0.7510 (mmp) REVERT: B 345 ILE cc_start: 0.8845 (mm) cc_final: 0.8224 (mm) REVERT: B 421 MET cc_start: 0.8707 (mmp) cc_final: 0.8459 (mmm) REVERT: B 479 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7893 (mmt-90) REVERT: B 513 GLN cc_start: 0.8381 (tt0) cc_final: 0.7614 (tm-30) REVERT: C 47 MET cc_start: 0.6785 (tpt) cc_final: 0.6467 (tpp) REVERT: C 56 ARG cc_start: 0.7571 (ttt-90) cc_final: 0.7117 (ttp80) REVERT: C 61 TRP cc_start: 0.6563 (m100) cc_final: 0.6001 (m-10) REVERT: C 156 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7351 (ttt) REVERT: C 232 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6968 (m90) REVERT: C 279 GLN cc_start: 0.8192 (mm-40) cc_final: 0.7839 (tp-100) REVERT: C 298 VAL cc_start: 0.8727 (t) cc_final: 0.8397 (t) REVERT: C 317 PHE cc_start: 0.8134 (t80) cc_final: 0.7751 (t80) REVERT: C 319 ASN cc_start: 0.8470 (m110) cc_final: 0.8120 (p0) REVERT: C 335 MET cc_start: 0.8186 (mmm) cc_final: 0.7849 (mmp) REVERT: C 402 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8722 (tt) REVERT: C 421 MET cc_start: 0.8796 (mmp) cc_final: 0.8576 (mmm) REVERT: C 479 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7885 (mmt-90) REVERT: D 47 MET cc_start: 0.6176 (tpt) cc_final: 0.5962 (tpp) REVERT: D 72 MET cc_start: 0.8577 (mmt) cc_final: 0.8355 (mmp) REVERT: D 126 LEU cc_start: 0.9049 (mt) cc_final: 0.8732 (tt) REVERT: D 147 GLU cc_start: 0.6455 (mt-10) cc_final: 0.5544 (mt-10) REVERT: D 232 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6929 (m-70) REVERT: D 240 ASP cc_start: 0.7304 (t0) cc_final: 0.6681 (t0) REVERT: D 298 VAL cc_start: 0.8460 (t) cc_final: 0.8260 (t) REVERT: D 317 PHE cc_start: 0.8040 (t80) cc_final: 0.7530 (t80) REVERT: D 319 ASN cc_start: 0.8480 (m110) cc_final: 0.8086 (p0) REVERT: D 344 MET cc_start: 0.8226 (ttm) cc_final: 0.7902 (ttp) REVERT: D 345 ILE cc_start: 0.8582 (mm) cc_final: 0.7974 (mm) REVERT: D 460 MET cc_start: 0.8333 (ttm) cc_final: 0.8073 (mtm) REVERT: D 479 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8195 (mmt-90) outliers start: 89 outliers final: 33 residues processed: 413 average time/residue: 0.1289 time to fit residues: 79.1533 Evaluate side-chains 328 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 284 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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: 5.9990 chunk 124 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN A 445 ASN A 456 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 ASN ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 ASN D 445 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.163201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120643 restraints weight = 22682.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.120394 restraints weight = 16467.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121751 restraints weight = 14154.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.122954 restraints weight = 10559.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123256 restraints weight = 9621.081| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16156 Z= 0.162 Angle : 0.597 9.555 21856 Z= 0.319 Chirality : 0.042 0.238 2492 Planarity : 0.003 0.040 2676 Dihedral : 5.554 40.139 2236 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 5.00 % Allowed : 21.78 % Favored : 73.22 % 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: 0.06 (0.19), residues: 1880 helix: 1.09 (0.15), residues: 1116 sheet: -1.05 (0.29), residues: 256 loop : -1.61 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 231 TYR 0.014 0.001 TYR D 398 PHE 0.021 0.002 PHE A 497 TRP 0.008 0.001 TRP B 272 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00354 (16148) covalent geometry : angle 0.57585 (21832) hydrogen bonds : bond 0.04967 ( 1026) hydrogen bonds : angle 4.91505 ( 3078) link_NAG-ASN : bond 0.00885 ( 8) link_NAG-ASN : angle 4.74772 ( 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 387 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 300 time to evaluate : 0.567 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 46 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.8137 (t80) REVERT: A 76 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8458 (tp40) REVERT: A 147 GLU cc_start: 0.6668 (mt-10) cc_final: 0.5677 (mt-10) REVERT: A 174 THR cc_start: 0.7488 (p) cc_final: 0.7266 (t) REVERT: A 181 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8702 (mp) REVERT: A 232 HIS cc_start: 0.7154 (OUTLIER) cc_final: 0.6752 (m90) REVERT: A 240 ASP cc_start: 0.7397 (t0) cc_final: 0.6907 (t0) REVERT: A 283 HIS cc_start: 0.8484 (OUTLIER) cc_final: 0.7663 (p90) REVERT: A 315 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8245 (mm-40) REVERT: A 317 PHE cc_start: 0.8032 (t80) cc_final: 0.7788 (t80) REVERT: A 319 ASN cc_start: 0.8421 (m110) cc_final: 0.8189 (p0) REVERT: A 335 MET cc_start: 0.7728 (mmm) cc_final: 0.7276 (mmp) REVERT: A 345 ILE cc_start: 0.8687 (mm) cc_final: 0.8473 (mm) REVERT: B 156 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: B 226 ASN cc_start: 0.8256 (t0) cc_final: 0.8034 (t0) REVERT: B 232 HIS cc_start: 0.7462 (OUTLIER) cc_final: 0.7060 (m90) REVERT: B 283 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7355 (p90) REVERT: B 335 MET cc_start: 0.7666 (mmm) cc_final: 0.7335 (mmp) REVERT: B 344 MET cc_start: 0.7669 (ttm) cc_final: 0.7419 (ttm) REVERT: B 421 MET cc_start: 0.8805 (mmp) cc_final: 0.8451 (mmp) REVERT: B 446 MET cc_start: 0.8528 (mtp) cc_final: 0.8233 (ttp) REVERT: B 450 CYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8373 (t) REVERT: B 479 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7747 (mmt-90) REVERT: C 56 ARG cc_start: 0.7670 (ttt-90) cc_final: 0.7230 (ttp80) REVERT: C 232 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6978 (m90) REVERT: C 240 ASP cc_start: 0.7663 (t0) cc_final: 0.7446 (t0) REVERT: C 314 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7712 (tm-30) REVERT: C 317 PHE cc_start: 0.8109 (t80) cc_final: 0.7852 (t80) REVERT: C 319 ASN cc_start: 0.8238 (m110) cc_final: 0.8035 (p0) REVERT: C 335 MET cc_start: 0.8000 (mmm) cc_final: 0.7682 (mmp) REVERT: C 337 PHE cc_start: 0.7884 (m-80) cc_final: 0.7594 (m-80) REVERT: C 421 MET cc_start: 0.8794 (mmp) cc_final: 0.8399 (mmp) REVERT: C 424 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 479 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8203 (tpp80) REVERT: D 126 LEU cc_start: 0.9109 (mt) cc_final: 0.8741 (tt) REVERT: D 147 GLU cc_start: 0.6741 (mt-10) cc_final: 0.5918 (mt-10) REVERT: D 232 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6879 (m-70) REVERT: D 240 ASP cc_start: 0.7452 (t0) cc_final: 0.6910 (t0) REVERT: D 271 ASP cc_start: 0.7922 (t0) cc_final: 0.7433 (t0) REVERT: D 298 VAL cc_start: 0.8650 (t) cc_final: 0.8271 (t) REVERT: D 315 GLN cc_start: 0.8317 (mm110) cc_final: 0.7709 (mm-40) REVERT: D 317 PHE cc_start: 0.8042 (t80) cc_final: 0.7659 (t80) REVERT: D 319 ASN cc_start: 0.8329 (m110) cc_final: 0.8083 (p0) REVERT: D 344 MET cc_start: 0.8203 (ttm) cc_final: 0.7978 (ttp) REVERT: D 345 ILE cc_start: 0.8628 (mm) cc_final: 0.8327 (mm) REVERT: D 424 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8409 (tp) REVERT: D 450 CYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7968 (t) outliers start: 87 outliers final: 42 residues processed: 362 average time/residue: 0.1180 time to fit residues: 65.3911 Evaluate side-chains 328 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 270 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 76 GLN 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 253 SER 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 392 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 493 ILE Chi-restraints excluded: chain B residue 46 PHE 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 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 479 ARG 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 400 LEU 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 446 MET Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 479 ARG 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 283 HIS Chi-restraints excluded: chain D residue 294 LEU 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 446 MET Chi-restraints excluded: chain D residue 450 CYS 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: 5.9990 chunk 178 optimal weight: 0.7980 chunk 166 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 HIS A 281 ASN B 100 HIS C 100 HIS C 281 ASN D 100 HIS D 281 ASN D 312 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.164083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121415 restraints weight = 22649.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122130 restraints weight = 17040.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123535 restraints weight = 13469.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126243 restraints weight = 10754.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126487 restraints weight = 9279.030| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4329 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= 0.155 Angle : 0.572 12.037 21856 Z= 0.301 Chirality : 0.041 0.220 2492 Planarity : 0.003 0.071 2676 Dihedral : 5.344 39.354 2236 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.40 % Allowed : 22.41 % Favored : 72.18 % 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: 0.58 (0.19), residues: 1880 helix: 1.53 (0.15), residues: 1120 sheet: -0.79 (0.28), residues: 280 loop : -1.55 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 231 TYR 0.015 0.001 TYR D 481 PHE 0.023 0.002 PHE B 317 TRP 0.009 0.001 TRP B 272 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00342 (16148) covalent geometry : angle 0.54550 (21832) hydrogen bonds : bond 0.04651 ( 1026) hydrogen bonds : angle 4.66456 ( 3078) link_NAG-ASN : bond 0.00531 ( 8) link_NAG-ASN : angle 5.17652 ( 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 384 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 290 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8257 (t80) REVERT: A 72 MET cc_start: 0.8366 (mmp) cc_final: 0.8142 (mmm) REVERT: A 147 GLU cc_start: 0.6699 (mt-10) cc_final: 0.5443 (mt-10) REVERT: A 181 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8608 (mp) REVERT: A 232 HIS cc_start: 0.7163 (OUTLIER) cc_final: 0.6784 (m-70) REVERT: A 283 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7599 (p90) REVERT: A 317 PHE cc_start: 0.7932 (t80) cc_final: 0.7721 (t80) REVERT: A 335 MET cc_start: 0.7619 (mmm) cc_final: 0.7222 (mmp) REVERT: A 344 MET cc_start: 0.8111 (ttm) cc_final: 0.7805 (ttm) REVERT: A 424 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8563 (tp) REVERT: A 450 CYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8034 (t) REVERT: A 467 MET cc_start: 0.8488 (mmm) cc_final: 0.8220 (mmm) REVERT: B 46 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8477 (t80) REVERT: B 156 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7254 (ttt) REVERT: B 226 ASN cc_start: 0.8340 (t0) cc_final: 0.8059 (t0) REVERT: B 232 HIS cc_start: 0.7349 (OUTLIER) cc_final: 0.6942 (m90) REVERT: B 240 ASP cc_start: 0.7602 (t0) cc_final: 0.7315 (t0) REVERT: B 283 HIS cc_start: 0.8217 (OUTLIER) cc_final: 0.7254 (p90) REVERT: B 335 MET cc_start: 0.7985 (mmm) cc_final: 0.7652 (mmp) REVERT: B 345 ILE cc_start: 0.8839 (mm) cc_final: 0.8567 (mm) REVERT: B 446 MET cc_start: 0.8481 (mtp) cc_final: 0.8280 (ttp) REVERT: B 450 CYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8036 (t) REVERT: B 476 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8878 (tt) REVERT: B 479 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7839 (mmp80) REVERT: C 44 PHE cc_start: 0.6687 (OUTLIER) cc_final: 0.5718 (p90) REVERT: C 56 ARG cc_start: 0.7659 (ttt-90) cc_final: 0.7171 (ttp80) REVERT: C 232 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6908 (m90) REVERT: C 314 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 317 PHE cc_start: 0.8054 (t80) cc_final: 0.7803 (t80) REVERT: C 335 MET cc_start: 0.8082 (mmm) cc_final: 0.7796 (mmp) REVERT: C 424 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8348 (tp) REVERT: C 459 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7893 (t0) REVERT: C 479 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8159 (tpp80) REVERT: D 232 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6856 (m-70) REVERT: D 315 GLN cc_start: 0.7990 (mm110) cc_final: 0.7521 (mm-40) REVERT: D 317 PHE cc_start: 0.7917 (t80) cc_final: 0.7684 (t80) REVERT: D 421 MET cc_start: 0.8926 (mmp) cc_final: 0.8596 (mmp) REVERT: D 424 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8457 (tp) REVERT: D 450 CYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8033 (t) REVERT: D 459 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7863 (t0) REVERT: D 460 MET cc_start: 0.8300 (ttm) cc_final: 0.8096 (mtt) outliers start: 94 outliers final: 46 residues processed: 358 average time/residue: 0.1126 time to fit residues: 62.3308 Evaluate side-chains 323 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 255 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 PHE Chi-restraints excluded: chain A residue 110 MET 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 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 400 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 478 SER Chi-restraints excluded: chain A residue 479 ARG Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 172 ASN 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 400 LEU 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 44 PHE Chi-restraints excluded: chain C residue 88 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 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 446 MET Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 494 LEU 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 400 LEU Chi-restraints excluded: chain D residue 424 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 478 SER 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: 0.9980 chunk 167 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 chunk 55 optimal weight: 0.0870 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3944 r_free = 0.3944 target = 0.166009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123508 restraints weight = 22621.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122834 restraints weight = 16203.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124191 restraints weight = 17428.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126573 restraints weight = 11578.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126756 restraints weight = 9764.283| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4710 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= 0.124 Angle : 0.555 11.587 21856 Z= 0.289 Chirality : 0.040 0.222 2492 Planarity : 0.003 0.044 2676 Dihedral : 5.114 39.098 2236 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.57 % Allowed : 22.93 % Favored : 71.49 % 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: 0.84 (0.19), residues: 1880 helix: 1.73 (0.15), residues: 1120 sheet: -0.69 (0.29), residues: 280 loop : -1.46 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 231 TYR 0.015 0.001 TYR D 481 PHE 0.023 0.002 PHE B 317 TRP 0.008 0.001 TRP B 272 HIS 0.002 0.001 HIS C 252 Details of bonding type rmsd covalent geometry : bond 0.00258 (16148) covalent geometry : angle 0.52412 (21832) hydrogen bonds : bond 0.04302 ( 1026) hydrogen bonds : angle 4.53067 ( 3078) link_NAG-ASN : bond 0.01020 ( 8) link_NAG-ASN : angle 5.53715 ( 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 383 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8272 (mmp) cc_final: 0.8061 (mmm) REVERT: A 232 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6756 (m-70) REVERT: A 283 HIS cc_start: 0.8556 (OUTLIER) cc_final: 0.7585 (p90) REVERT: A 292 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8780 (p) REVERT: A 317 PHE cc_start: 0.7963 (t80) cc_final: 0.7716 (t80) REVERT: A 326 LYS cc_start: 0.8135 (mttt) cc_final: 0.7605 (mtmt) REVERT: A 335 MET cc_start: 0.7693 (mmm) cc_final: 0.7325 (mmp) REVERT: A 424 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8534 (tp) REVERT: A 450 CYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8043 (t) REVERT: A 467 MET cc_start: 0.8490 (mmm) cc_final: 0.8228 (mmm) REVERT: A 476 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8847 (tt) REVERT: B 46 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8443 (t80) REVERT: B 226 ASN cc_start: 0.8295 (t0) cc_final: 0.7943 (t0) REVERT: B 232 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6921 (m90) REVERT: B 240 ASP cc_start: 0.7537 (t0) cc_final: 0.7255 (t0) REVERT: B 283 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7357 (p90) REVERT: B 317 PHE cc_start: 0.7960 (t80) cc_final: 0.7722 (t80) REVERT: B 335 MET cc_start: 0.7982 (mmm) cc_final: 0.7622 (mmp) REVERT: B 337 PHE cc_start: 0.7935 (m-80) cc_final: 0.7679 (m-10) REVERT: B 479 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7798 (mmt-90) REVERT: C 44 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.5894 (p90) REVERT: C 56 ARG cc_start: 0.7662 (ttt-90) cc_final: 0.7105 (ttp80) REVERT: C 232 HIS cc_start: 0.7152 (OUTLIER) cc_final: 0.6840 (m-70) REVERT: C 315 GLN cc_start: 0.8378 (mm110) cc_final: 0.8175 (mm-40) REVERT: C 335 MET cc_start: 0.8084 (mmm) cc_final: 0.7797 (mmp) REVERT: C 390 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7879 (ttp-110) REVERT: C 424 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8364 (tp) REVERT: C 476 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8972 (tt) REVERT: C 479 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7668 (mmt-90) REVERT: D 232 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6809 (m-70) REVERT: D 240 ASP cc_start: 0.7375 (t0) cc_final: 0.7023 (t0) REVERT: D 317 PHE cc_start: 0.7678 (t80) cc_final: 0.7460 (t80) REVERT: D 386 LEU cc_start: 0.9084 (tt) cc_final: 0.8881 (tt) REVERT: D 390 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7855 (ttp-170) REVERT: D 421 MET cc_start: 0.8906 (mmp) cc_final: 0.8496 (mmm) REVERT: D 424 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8412 (tp) REVERT: D 459 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7747 (t0) REVERT: D 476 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8926 (tt) outliers start: 97 outliers final: 48 residues processed: 361 average time/residue: 0.1212 time to fit residues: 66.6521 Evaluate side-chains 335 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 CYS 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 400 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 B residue 46 PHE Chi-restraints excluded: chain B residue 172 ASN 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 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 478 SER Chi-restraints excluded: chain B residue 479 ARG Chi-restraints excluded: chain B residue 494 LEU Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 122 VAL 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 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 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 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 424 LEU Chi-restraints excluded: chain D residue 426 TYR Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain D residue 459 ASP 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 22 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN 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 = 0.3895 r_free = 0.3895 target = 0.161589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118563 restraints weight = 22490.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121763 restraints weight = 17046.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.122161 restraints weight = 14650.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123689 restraints weight = 10669.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.123746 restraints weight = 8983.723| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16156 Z= 0.232 Angle : 0.648 12.057 21856 Z= 0.338 Chirality : 0.043 0.217 2492 Planarity : 0.003 0.039 2676 Dihedral : 5.438 42.685 2236 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 6.21 % Allowed : 23.28 % Favored : 70.52 % 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: 0.68 (0.19), residues: 1880 helix: 1.60 (0.15), residues: 1120 sheet: -0.76 (0.28), residues: 276 loop : -1.50 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 231 TYR 0.018 0.002 TYR D 481 PHE 0.022 0.002 PHE A 497 TRP 0.012 0.001 TRP C 272 HIS 0.003 0.001 HIS C 438 Details of bonding type rmsd covalent geometry : bond 0.00530 (16148) covalent geometry : angle 0.61940 (21832) hydrogen bonds : bond 0.04885 ( 1026) hydrogen bonds : angle 4.74459 ( 3078) link_NAG-ASN : bond 0.00784 ( 8) link_NAG-ASN : angle 5.79005 ( 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 374 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 266 time to evaluate : 0.604 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: 0.6211 (tpp) cc_final: 0.5968 (tpp) REVERT: A 72 MET cc_start: 0.8366 (mmp) cc_final: 0.8075 (mmm) REVERT: A 232 HIS cc_start: 0.7139 (OUTLIER) cc_final: 0.6753 (m-70) REVERT: A 283 HIS cc_start: 0.8530 (OUTLIER) cc_final: 0.7694 (p90) REVERT: A 292 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8765 (p) REVERT: A 317 PHE cc_start: 0.7954 (t80) cc_final: 0.7633 (t80) REVERT: A 326 LYS cc_start: 0.8058 (mttt) cc_final: 0.7549 (mtmt) REVERT: A 335 MET cc_start: 0.7815 (mmm) cc_final: 0.7540 (mmp) REVERT: A 424 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8570 (tp) REVERT: A 450 CYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8419 (t) REVERT: A 467 MET cc_start: 0.8537 (mmm) cc_final: 0.8233 (mmm) REVERT: A 476 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8801 (tt) REVERT: B 46 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8414 (t80) REVERT: B 47 MET cc_start: 0.6482 (tpp) cc_final: 0.6186 (tpp) REVERT: B 56 ARG cc_start: 0.7494 (tmm160) cc_final: 0.5889 (ttt-90) REVERT: B 226 ASN cc_start: 0.8474 (t0) cc_final: 0.8161 (t0) REVERT: B 232 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6885 (m90) REVERT: B 240 ASP cc_start: 0.7609 (t0) cc_final: 0.7335 (t0) REVERT: B 283 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.7494 (p90) REVERT: B 317 PHE cc_start: 0.7968 (t80) cc_final: 0.7723 (t80) REVERT: B 335 MET cc_start: 0.8042 (mmm) cc_final: 0.7770 (mmp) REVERT: B 476 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8848 (tt) REVERT: B 479 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7488 (mpt180) REVERT: C 44 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5970 (p90) REVERT: C 56 ARG cc_start: 0.7684 (ttt-90) cc_final: 0.6930 (tmm160) REVERT: C 232 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6735 (m-70) REVERT: C 315 GLN cc_start: 0.8105 (mm110) cc_final: 0.7734 (mm-40) REVERT: C 335 MET cc_start: 0.8060 (mmm) cc_final: 0.7749 (mmp) REVERT: C 367 LEU cc_start: 0.8119 (mp) cc_final: 0.7889 (mm) REVERT: C 424 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8449 (tp) REVERT: C 476 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8863 (tt) REVERT: C 479 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7708 (mmt-90) REVERT: D 147 GLU cc_start: 0.6498 (mt-10) cc_final: 0.6258 (mt-10) REVERT: D 232 HIS cc_start: 0.6998 (OUTLIER) cc_final: 0.6728 (m-70) REVERT: D 240 ASP cc_start: 0.7564 (t0) cc_final: 0.7213 (t0) REVERT: D 317 PHE cc_start: 0.7721 (t80) cc_final: 0.7478 (t80) REVERT: D 421 MET cc_start: 0.8898 (mmp) cc_final: 0.8663 (mmm) REVERT: D 424 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8462 (tp) REVERT: D 476 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8883 (tt) outliers start: 108 outliers final: 74 residues processed: 354 average time/residue: 0.1144 time to fit residues: 62.0587 Evaluate side-chains 343 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 250 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 116 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 172 ASN 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 400 LEU Chi-restraints excluded: chain A residue 403 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 A residue 522 ARG Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 50 CYS 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 172 ASN 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 C residue 44 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 122 VAL 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 253 SER 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 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 D residue 50 CYS Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 110 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 126 LEU 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 362 ILE Chi-restraints excluded: chain D residue 373 CYS 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 480 ILE 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: 0.8980 chunk 68 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 108 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 456 ASN C 273 HIS C 281 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.166964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.123914 restraints weight = 22311.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124938 restraints weight = 13838.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126083 restraints weight = 11507.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.126514 restraints weight = 9492.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.126860 restraints weight = 9175.612| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.5130 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= 0.121 Angle : 0.584 12.099 21856 Z= 0.296 Chirality : 0.040 0.233 2492 Planarity : 0.003 0.042 2676 Dihedral : 5.100 42.372 2236 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.71 % Allowed : 24.83 % Favored : 70.46 % 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: 0.97 (0.19), residues: 1880 helix: 1.85 (0.15), residues: 1120 sheet: -0.66 (0.29), residues: 276 loop : -1.40 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.014 0.001 TYR D 481 PHE 0.017 0.001 PHE B 337 TRP 0.010 0.001 TRP C 272 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00247 (16148) covalent geometry : angle 0.55106 (21832) hydrogen bonds : bond 0.04219 ( 1026) hydrogen bonds : angle 4.51671 ( 3078) link_NAG-ASN : bond 0.00935 ( 8) link_NAG-ASN : angle 5.82271 ( 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 364 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 282 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 MET cc_start: 0.8134 (mmp) cc_final: 0.7916 (mmm) REVERT: A 232 HIS cc_start: 0.7143 (OUTLIER) cc_final: 0.6743 (m-70) REVERT: A 283 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.7597 (p90) REVERT: A 317 PHE cc_start: 0.7954 (t80) cc_final: 0.7746 (t80) REVERT: A 335 MET cc_start: 0.7679 (mmm) cc_final: 0.7273 (mmp) REVERT: A 467 MET cc_start: 0.8433 (mmm) cc_final: 0.8101 (mmm) REVERT: A 476 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 38 MET cc_start: 0.6865 (ppp) cc_final: 0.6506 (ppp) REVERT: B 56 ARG cc_start: 0.7245 (tmm160) cc_final: 0.5650 (ptm-80) REVERT: B 226 ASN cc_start: 0.8459 (t0) cc_final: 0.8094 (t0) REVERT: B 232 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6861 (m-70) REVERT: B 240 ASP cc_start: 0.7491 (t0) cc_final: 0.7227 (t0) REVERT: B 283 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.7431 (p90) REVERT: B 317 PHE cc_start: 0.7902 (t80) cc_final: 0.7600 (t80) REVERT: B 335 MET cc_start: 0.7994 (mmm) cc_final: 0.7642 (mmp) REVERT: B 479 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7735 (mmt-90) REVERT: C 38 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6996 (tmm) REVERT: C 44 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5937 (p90) REVERT: C 56 ARG cc_start: 0.7718 (ttt-90) cc_final: 0.6951 (tmm160) REVERT: C 232 HIS cc_start: 0.7060 (OUTLIER) cc_final: 0.6691 (m-70) REVERT: C 335 MET cc_start: 0.7709 (mmm) cc_final: 0.7307 (mmp) REVERT: C 390 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7930 (ttp-110) REVERT: C 424 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8294 (tp) REVERT: C 479 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7688 (mmt-90) REVERT: D 38 MET cc_start: 0.7006 (tmm) cc_final: 0.6791 (tmm) REVERT: D 45 PHE cc_start: 0.7477 (t80) cc_final: 0.7168 (t80) REVERT: D 231 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7625 (mtp-110) REVERT: D 232 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6633 (m-70) REVERT: D 240 ASP cc_start: 0.7363 (t0) cc_final: 0.6968 (t0) REVERT: D 281 ASN cc_start: 0.6632 (OUTLIER) cc_final: 0.6283 (m110) REVERT: D 386 LEU cc_start: 0.9091 (tt) cc_final: 0.8861 (tt) REVERT: D 390 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7886 (ttp-110) REVERT: D 421 MET cc_start: 0.8859 (mmp) cc_final: 0.8476 (mmm) REVERT: D 424 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8321 (tp) REVERT: D 476 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8895 (tt) outliers start: 82 outliers final: 48 residues processed: 349 average time/residue: 0.1201 time to fit residues: 63.6894 Evaluate side-chains 327 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 262 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 494 LEU Chi-restraints excluded: chain A residue 522 ARG Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 88 VAL 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 494 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 122 VAL 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 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 373 CYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 142 optimal weight: 0.5980 chunk 176 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3952 r_free = 0.3952 target = 0.167018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.124523 restraints weight = 22467.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124168 restraints weight = 15355.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125557 restraints weight = 13745.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126670 restraints weight = 10139.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.127012 restraints weight = 9446.225| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.5263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16156 Z= 0.126 Angle : 0.587 12.140 21856 Z= 0.296 Chirality : 0.040 0.231 2492 Planarity : 0.003 0.043 2676 Dihedral : 5.038 41.555 2236 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Rotamer: Outliers : 4.31 % Allowed : 25.52 % Favored : 70.17 % 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 (0.19), residues: 1880 helix: 1.93 (0.15), residues: 1120 sheet: -0.56 (0.30), residues: 276 loop : -1.37 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.014 0.001 TYR D 481 PHE 0.016 0.001 PHE B 497 TRP 0.009 0.001 TRP C 272 HIS 0.003 0.001 HIS C 283 Details of bonding type rmsd covalent geometry : bond 0.00268 (16148) covalent geometry : angle 0.55571 (21832) hydrogen bonds : bond 0.04140 ( 1026) hydrogen bonds : angle 4.48450 ( 3078) link_NAG-ASN : bond 0.00978 ( 8) link_NAG-ASN : angle 5.77339 ( 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 346 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 271 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6197 (tpp) cc_final: 0.5977 (tpp) REVERT: A 232 HIS cc_start: 0.7166 (OUTLIER) cc_final: 0.6752 (m90) REVERT: A 283 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.7802 (p90) REVERT: A 317 PHE cc_start: 0.7930 (t80) cc_final: 0.7705 (t80) REVERT: A 335 MET cc_start: 0.7671 (mmm) cc_final: 0.7309 (mmp) REVERT: A 424 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8499 (tp) REVERT: A 476 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8890 (tt) REVERT: B 38 MET cc_start: 0.6888 (ppp) cc_final: 0.6528 (ppp) REVERT: B 47 MET cc_start: 0.6584 (tpp) cc_final: 0.6304 (tpp) REVERT: B 56 ARG cc_start: 0.7229 (tmm160) cc_final: 0.5652 (ptm-80) REVERT: B 186 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6976 (m-10) REVERT: B 226 ASN cc_start: 0.8400 (t0) cc_final: 0.8011 (t0) REVERT: B 232 HIS cc_start: 0.7216 (OUTLIER) cc_final: 0.6753 (m90) REVERT: B 240 ASP cc_start: 0.7473 (t0) cc_final: 0.7213 (t0) REVERT: B 283 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7425 (p90) REVERT: B 317 PHE cc_start: 0.7942 (t80) cc_final: 0.7597 (t80) REVERT: B 335 MET cc_start: 0.8007 (mmm) cc_final: 0.7677 (mmp) REVERT: B 460 MET cc_start: 0.8202 (ttm) cc_final: 0.7972 (mtt) REVERT: B 479 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7714 (mmt-90) REVERT: B 516 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: C 38 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.7004 (tmm) REVERT: C 44 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.5868 (p90) REVERT: C 232 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.6617 (m-70) REVERT: C 335 MET cc_start: 0.7766 (mmm) cc_final: 0.7357 (mmp) REVERT: C 424 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8291 (tp) REVERT: C 459 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7692 (t0) REVERT: C 460 MET cc_start: 0.8199 (ttm) cc_final: 0.7953 (mtt) REVERT: C 479 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7630 (mmt-90) REVERT: D 45 PHE cc_start: 0.7529 (t80) cc_final: 0.7195 (t80) REVERT: D 231 ARG cc_start: 0.7875 (mmm-85) cc_final: 0.7558 (mtp-110) REVERT: D 232 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6626 (m-70) REVERT: D 281 ASN cc_start: 0.6709 (OUTLIER) cc_final: 0.6311 (m-40) REVERT: D 390 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7962 (ttp-170) REVERT: D 421 MET cc_start: 0.8859 (mmp) cc_final: 0.8482 (mmm) REVERT: D 424 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8265 (tp) REVERT: D 476 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8899 (tt) outliers start: 75 outliers final: 48 residues processed: 323 average time/residue: 0.1212 time to fit residues: 59.7651 Evaluate side-chains 328 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 260 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 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 424 LEU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain A residue 476 LEU 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 522 ARG Chi-restraints excluded: chain B residue 46 PHE 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 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 494 LEU 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 110 MET Chi-restraints excluded: chain C residue 122 VAL 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 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 446 MET Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 479 ARG Chi-restraints excluded: chain C residue 489 PHE 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 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 446 MET 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 14 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN C 456 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 = 0.3960 r_free = 0.3960 target = 0.167804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125426 restraints weight = 22302.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123921 restraints weight = 16296.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125311 restraints weight = 18326.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126401 restraints weight = 11758.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.127230 restraints weight = 10429.048| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5400 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= 0.121 Angle : 0.580 12.125 21856 Z= 0.291 Chirality : 0.040 0.243 2492 Planarity : 0.003 0.043 2676 Dihedral : 4.934 41.513 2236 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Rotamer: Outliers : 4.25 % Allowed : 25.46 % Favored : 70.29 % 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: 1.22 (0.19), residues: 1880 helix: 1.93 (0.15), residues: 1148 sheet: -0.34 (0.31), residues: 268 loop : -1.32 (0.27), residues: 464 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 0.016 0.001 PHE A 497 TRP 0.009 0.001 TRP A 475 HIS 0.002 0.001 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00254 (16148) covalent geometry : angle 0.54897 (21832) hydrogen bonds : bond 0.04008 ( 1026) hydrogen bonds : angle 4.42795 ( 3078) link_NAG-ASN : bond 0.00934 ( 8) link_NAG-ASN : angle 5.70371 ( 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 350 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 276 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.6217 (tpp) cc_final: 0.5977 (tpp) REVERT: A 186 PHE cc_start: 0.7275 (t80) cc_final: 0.7033 (t80) REVERT: A 232 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6808 (m-70) REVERT: A 283 HIS cc_start: 0.8559 (OUTLIER) cc_final: 0.7658 (p90) REVERT: A 317 PHE cc_start: 0.7914 (t80) cc_final: 0.7687 (t80) REVERT: A 335 MET cc_start: 0.7739 (mmm) cc_final: 0.7307 (mmp) REVERT: A 424 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8510 (tp) REVERT: A 476 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8884 (tt) REVERT: B 38 MET cc_start: 0.6863 (ppp) cc_final: 0.6490 (ppp) REVERT: B 47 MET cc_start: 0.6555 (tpp) cc_final: 0.6300 (tpp) REVERT: B 56 ARG cc_start: 0.7192 (tmm160) cc_final: 0.5622 (ptm-80) REVERT: B 186 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6844 (m-10) REVERT: B 226 ASN cc_start: 0.8354 (t0) cc_final: 0.7967 (t0) REVERT: B 232 HIS cc_start: 0.7179 (OUTLIER) cc_final: 0.6773 (m-70) REVERT: B 283 HIS cc_start: 0.8392 (OUTLIER) cc_final: 0.7344 (p90) REVERT: B 317 PHE cc_start: 0.7948 (t80) cc_final: 0.7589 (t80) REVERT: B 335 MET cc_start: 0.7981 (mmm) cc_final: 0.7649 (mmp) REVERT: B 460 MET cc_start: 0.8170 (ttm) cc_final: 0.7928 (mtt) REVERT: B 479 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7691 (mmt-90) REVERT: B 516 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: C 38 MET cc_start: 0.7241 (OUTLIER) cc_final: 0.6999 (tmm) REVERT: C 44 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.5909 (p90) REVERT: C 232 HIS cc_start: 0.6898 (OUTLIER) cc_final: 0.6546 (m90) REVERT: C 335 MET cc_start: 0.7794 (mmm) cc_final: 0.7385 (mmp) REVERT: C 390 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7937 (ttp-110) REVERT: C 424 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8279 (tp) REVERT: C 460 MET cc_start: 0.8188 (ttm) cc_final: 0.7954 (mtt) REVERT: D 38 MET cc_start: 0.7320 (tmm) cc_final: 0.6863 (tmm) REVERT: D 231 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7453 (mtp-110) REVERT: D 232 HIS cc_start: 0.6901 (OUTLIER) cc_final: 0.6625 (m90) REVERT: D 281 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6720 (m110) REVERT: D 390 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7720 (ttp-170) REVERT: D 421 MET cc_start: 0.8815 (mmp) cc_final: 0.8391 (mmm) REVERT: D 424 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8266 (tp) REVERT: D 476 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8868 (tt) outliers start: 74 outliers final: 50 residues processed: 326 average time/residue: 0.1236 time to fit residues: 61.3063 Evaluate side-chains 327 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 424 LEU Chi-restraints excluded: chain A residue 426 TYR 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 494 LEU 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 479 ARG Chi-restraints excluded: chain B residue 494 LEU 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 110 MET Chi-restraints excluded: chain C residue 122 VAL 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 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 C residue 489 PHE 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 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 446 MET 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 150 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 166 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN D 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.168480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.128892 restraints weight = 21585.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127852 restraints weight = 16871.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129320 restraints weight = 14727.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.130067 restraints weight = 11888.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130514 restraints weight = 11545.422| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16156 Z= 0.219 Angle : 0.660 12.057 21856 Z= 0.335 Chirality : 0.043 0.235 2492 Planarity : 0.003 0.039 2676 Dihedral : 5.055 43.523 2232 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Rotamer: Outliers : 4.14 % Allowed : 26.26 % Favored : 69.60 % 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: 1.03 (0.19), residues: 1880 helix: 1.74 (0.15), residues: 1144 sheet: -0.39 (0.30), residues: 276 loop : -1.29 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 479 TYR 0.018 0.002 TYR D 481 PHE 0.021 0.002 PHE A 497 TRP 0.015 0.001 TRP C 272 HIS 0.002 0.001 HIS D 438 Details of bonding type rmsd covalent geometry : bond 0.00503 (16148) covalent geometry : angle 0.63296 (21832) hydrogen bonds : bond 0.04651 ( 1026) hydrogen bonds : angle 4.63270 ( 3078) link_NAG-ASN : bond 0.00850 ( 8) link_NAG-ASN : angle 5.63306 ( 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 334 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 262 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.5935 (p90) REVERT: A 232 HIS cc_start: 0.7180 (OUTLIER) cc_final: 0.6838 (m-70) REVERT: A 283 HIS cc_start: 0.8542 (OUTLIER) cc_final: 0.7608 (p90) REVERT: A 317 PHE cc_start: 0.7831 (t80) cc_final: 0.7582 (t80) REVERT: A 335 MET cc_start: 0.7791 (mmm) cc_final: 0.7361 (mmp) REVERT: A 424 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8656 (tp) REVERT: A 467 MET cc_start: 0.8441 (mmm) cc_final: 0.8130 (mmm) REVERT: A 476 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8966 (tt) REVERT: B 46 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8254 (t80) REVERT: B 47 MET cc_start: 0.6695 (tpp) cc_final: 0.6477 (tpp) REVERT: B 56 ARG cc_start: 0.7140 (tmm160) cc_final: 0.5618 (ptm-80) REVERT: B 226 ASN cc_start: 0.8493 (t0) cc_final: 0.8164 (t0) REVERT: B 232 HIS cc_start: 0.7213 (OUTLIER) cc_final: 0.6850 (m-70) REVERT: B 283 HIS cc_start: 0.8270 (OUTLIER) cc_final: 0.7410 (p90) REVERT: B 317 PHE cc_start: 0.8002 (t80) cc_final: 0.7669 (t80) REVERT: B 335 MET cc_start: 0.8021 (mmm) cc_final: 0.7694 (mmp) REVERT: B 479 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7716 (mmt-90) REVERT: B 516 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6998 (m-80) REVERT: C 44 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5891 (p90) REVERT: C 232 HIS cc_start: 0.6922 (OUTLIER) cc_final: 0.6713 (m-70) REVERT: C 335 MET cc_start: 0.7692 (mmm) cc_final: 0.7360 (mmp) REVERT: C 390 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7773 (ttp-170) REVERT: C 424 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8455 (tp) REVERT: D 38 MET cc_start: 0.6960 (tmm) cc_final: 0.6733 (tmm) REVERT: D 231 ARG cc_start: 0.7763 (mmm-85) cc_final: 0.7524 (mtp-110) REVERT: D 232 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6682 (m-70) REVERT: D 424 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8457 (tp) REVERT: D 460 MET cc_start: 0.8517 (ttm) cc_final: 0.8204 (mtm) REVERT: D 476 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9010 (tt) outliers start: 72 outliers final: 50 residues processed: 315 average time/residue: 0.1244 time to fit residues: 59.6182 Evaluate side-chains 323 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 256 time to evaluate : 0.643 ------------------------------------------------------------------------------- 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 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 424 LEU Chi-restraints excluded: chain A residue 426 TYR 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 494 LEU Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 122 VAL 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 494 LEU Chi-restraints excluded: chain B residue 516 PHE Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 122 VAL 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 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 C residue 478 SER 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 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 446 MET 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 489 PHE Chi-restraints excluded: chain D residue 494 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.166512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.122931 restraints weight = 22280.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.124513 restraints weight = 13929.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.125330 restraints weight = 13327.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125874 restraints weight = 9646.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.126456 restraints weight = 8961.214| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5457 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= 0.133 Angle : 0.616 12.151 21856 Z= 0.306 Chirality : 0.041 0.247 2492 Planarity : 0.003 0.042 2676 Dihedral : 4.878 43.935 2232 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.02 % Favored : 97.93 % Rotamer: Outliers : 3.91 % Allowed : 26.55 % 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: 1.15 (0.19), residues: 1880 helix: 1.88 (0.15), residues: 1136 sheet: -0.26 (0.31), residues: 268 loop : -1.35 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 231 TYR 0.015 0.001 TYR D 481 PHE 0.016 0.001 PHE A 497 TRP 0.012 0.001 TRP C 475 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00287 (16148) covalent geometry : angle 0.58750 (21832) hydrogen bonds : bond 0.04222 ( 1026) hydrogen bonds : angle 4.51940 ( 3078) link_NAG-ASN : bond 0.00873 ( 8) link_NAG-ASN : angle 5.62762 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.30 seconds wall clock time: 44 minutes 4.49 seconds (2644.49 seconds total)