Starting phenix.real_space_refine on Fri Jul 3 14:57:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.map" model { file = "/net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfw_23307/07_2026/7lfw_23307.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 76 5.16 5 C 9684 2.51 5 N 2396 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 2, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.24, per 1000 atoms: 0.22 Number of scatterers: 14846 At special positions: 0 Unit cell: (96.485, 96.485, 114.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 76 16.00 P 4 15.00 O 2684 8.00 N 2396 7.00 C 9684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 660.8 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 66.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.523A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.259A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.261A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.840A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.769A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.253A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 4.235A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.253A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.537A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.840A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.769A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA D 406 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 407 " --> pdb=" O MET D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 591 through 605 removed outlier: 3.642A pdb=" N LYS D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 removed outlier: 7.057A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR B 505 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER B 567 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 removed outlier: 7.057A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.21 Time building geometry restraints manager: 1.61 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: 4358 1.34 - 1.45: 2369 1.45 - 1.57: 8333 1.57 - 1.69: 8 1.69 - 1.81: 128 Bond restraints: 15196 Sorted by residual: bond pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O1A PCG C 701 " pdb=" PA PCG C 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1' PCG B 701 " pdb=" O4' PCG B 701 " ideal model delta sigma weight residual 1.409 1.477 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 15191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 20211 1.86 - 3.71: 277 3.71 - 5.57: 72 5.57 - 7.43: 24 7.43 - 9.28: 24 Bond angle restraints: 20608 Sorted by residual: angle pdb=" N ARG C 291 " pdb=" CA ARG C 291 " pdb=" C ARG C 291 " ideal model delta sigma weight residual 112.89 119.24 -6.35 1.24e+00 6.50e-01 2.62e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.21 -6.32 1.24e+00 6.50e-01 2.60e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.16 -6.27 1.24e+00 6.50e-01 2.56e+01 angle pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " pdb=" O3' PCG B 701 " ideal model delta sigma weight residual 100.83 110.11 -9.28 3.00e+00 1.11e-01 9.57e+00 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 8794 28.99 - 57.99: 286 57.99 - 86.98: 8 86.98 - 115.97: 4 115.97 - 144.96: 12 Dihedral angle restraints: 9104 sinusoidal: 3788 harmonic: 5316 Sorted by residual: dihedral pdb=" C3' PCG B 701 " pdb=" O3' PCG B 701 " pdb=" PA PCG B 701 " pdb=" O1A PCG B 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.63 -144.96 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG C 701 " pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O1A PCG C 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.65 -144.94 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG D 701 " pdb=" O3' PCG D 701 " pdb=" PA PCG D 701 " pdb=" O1A PCG D 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.68 -144.91 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2276 0.131 - 0.263: 28 0.263 - 0.394: 4 0.394 - 0.525: 0 0.525 - 0.657: 4 Chirality restraints: 2312 Sorted by residual: chirality pdb=" PA PCG B 701 " pdb=" O2A PCG B 701 " pdb=" O3' PCG B 701 " pdb=" O5' PCG B 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.36 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" PA PCG C 701 " pdb=" O2A PCG C 701 " pdb=" O3' PCG C 701 " pdb=" O5' PCG C 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" PA PCG D 701 " pdb=" O2A PCG D 701 " pdb=" O3' PCG D 701 " pdb=" O5' PCG D 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 2309 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C VAL D 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL D 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL D 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C VAL C 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL C 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 526 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C VAL B 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2644 2.76 - 3.30: 15656 3.30 - 3.83: 26907 3.83 - 4.37: 32515 4.37 - 4.90: 53421 Nonbonded interactions: 131143 Sorted by model distance: nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.227 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.319 3.040 ... (remaining 131138 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 701) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.840 Find NCS groups from input model: 0.240 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 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 : 0.005 0.105 15196 Z= 0.230 Angle : 0.696 9.283 20608 Z= 0.370 Chirality : 0.052 0.657 2312 Planarity : 0.003 0.028 2540 Dihedral : 14.963 144.963 5696 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.25 % Allowed : 2.72 % Favored : 97.04 % 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: -1.18 (0.19), residues: 1792 helix: -0.53 (0.14), residues: 1080 sheet: -1.26 (0.82), residues: 56 loop : -0.92 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 561 TYR 0.014 0.001 TYR C 349 PHE 0.014 0.002 PHE C 389 TRP 0.024 0.002 TRP C 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (15196) covalent geometry : angle 0.69617 / 0.37 (20608) hydrogen bonds : bond 0.12174 / 7.96 ( 904) hydrogen bonds : angle 6.69145 / 4.86 ( 2652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 0.453 Fit side-chains REVERT: A 266 ASN cc_start: 0.7431 (t0) cc_final: 0.7210 (t0) REVERT: A 428 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7404 (mptp) REVERT: A 450 GLU cc_start: 0.6476 (pt0) cc_final: 0.6115 (pp20) REVERT: A 496 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7094 (mt0) REVERT: A 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6228 (mptp) REVERT: B 266 ASN cc_start: 0.7432 (t0) cc_final: 0.7217 (t0) REVERT: B 428 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7399 (mptp) REVERT: B 450 GLU cc_start: 0.6477 (pt0) cc_final: 0.6118 (pp20) REVERT: B 496 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7107 (mt0) REVERT: B 605 LYS cc_start: 0.6441 (ptmt) cc_final: 0.6225 (mptp) REVERT: C 266 ASN cc_start: 0.7427 (t0) cc_final: 0.7206 (t0) REVERT: C 428 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7416 (mptp) REVERT: C 450 GLU cc_start: 0.6478 (pt0) cc_final: 0.6129 (pp20) REVERT: C 496 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7142 (mt0) REVERT: C 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6226 (mptp) REVERT: D 266 ASN cc_start: 0.7421 (t0) cc_final: 0.7182 (t0) REVERT: D 428 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7399 (mptp) REVERT: D 450 GLU cc_start: 0.6475 (pt0) cc_final: 0.6117 (pp20) REVERT: D 496 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7089 (mt0) REVERT: D 605 LYS cc_start: 0.6449 (ptmt) cc_final: 0.6219 (mptp) outliers start: 4 outliers final: 4 residues processed: 267 average time/residue: 0.6252 time to fit residues: 180.9009 Evaluate side-chains 174 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain D residue 291 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 238 ASN A 395 ASN A 402 ASN A 468 ASN A 534 GLN B 238 ASN B 302 ASN B 395 ASN B 402 ASN B 468 ASN B 534 GLN C 238 ASN C 395 ASN C 402 ASN C 468 ASN C 534 GLN D 238 ASN D 395 ASN D 402 ASN D 468 ASN D 534 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120356 restraints weight = 17652.967| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.73 r_work: 0.3125 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15196 Z= 0.129 Angle : 0.535 7.403 20608 Z= 0.279 Chirality : 0.041 0.157 2312 Planarity : 0.004 0.034 2540 Dihedral : 12.871 153.916 2136 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.74 % Allowed : 9.75 % Favored : 89.51 % 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: 0.46 (0.21), residues: 1792 helix: 0.89 (0.16), residues: 1068 sheet: -0.70 (0.68), residues: 56 loop : -0.44 (0.28), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.013 0.001 TYR B 349 PHE 0.012 0.001 PHE D 389 TRP 0.018 0.001 TRP C 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15196) covalent geometry : angle 0.53516 / 0.28 (20608) hydrogen bonds : bond 0.03947 / 2.56 ( 904) hydrogen bonds : angle 4.88662 / 3.53 ( 2652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 207 time to evaluate : 0.477 Fit side-chains REVERT: A 266 ASN cc_start: 0.7804 (t0) cc_final: 0.7533 (t0) REVERT: A 341 GLU cc_start: 0.7881 (tp30) cc_final: 0.7663 (tp30) REVERT: A 428 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7566 (mptt) REVERT: A 450 GLU cc_start: 0.6590 (pt0) cc_final: 0.6265 (pp20) REVERT: A 452 GLU cc_start: 0.7966 (tp30) cc_final: 0.7742 (tp30) REVERT: A 496 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7324 (mt0) REVERT: A 605 LYS cc_start: 0.6543 (ptmt) cc_final: 0.6230 (mptp) REVERT: B 266 ASN cc_start: 0.7810 (t0) cc_final: 0.7561 (t0) REVERT: B 428 LYS cc_start: 0.7903 (mtpt) cc_final: 0.7539 (mptp) REVERT: B 450 GLU cc_start: 0.6604 (pt0) cc_final: 0.6293 (pp20) REVERT: B 496 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7288 (mt0) REVERT: B 605 LYS cc_start: 0.6529 (ptmt) cc_final: 0.6216 (mptp) REVERT: C 266 ASN cc_start: 0.7764 (t0) cc_final: 0.7533 (t0) REVERT: C 428 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7597 (mptt) REVERT: C 450 GLU cc_start: 0.6581 (pt0) cc_final: 0.6268 (pp20) REVERT: C 452 GLU cc_start: 0.7982 (tp30) cc_final: 0.7752 (tp30) REVERT: C 496 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7299 (mt0) REVERT: C 605 LYS cc_start: 0.6522 (ptmt) cc_final: 0.6212 (mptp) REVERT: D 266 ASN cc_start: 0.7782 (t0) cc_final: 0.7523 (t0) REVERT: D 428 LYS cc_start: 0.7887 (mtpt) cc_final: 0.7576 (mptt) REVERT: D 450 GLU cc_start: 0.6561 (pt0) cc_final: 0.6253 (pp20) REVERT: D 452 GLU cc_start: 0.7977 (tp30) cc_final: 0.7749 (tp30) REVERT: D 496 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7349 (mt0) REVERT: D 605 LYS cc_start: 0.6557 (ptmt) cc_final: 0.6250 (mptp) outliers start: 12 outliers final: 4 residues processed: 208 average time/residue: 0.5481 time to fit residues: 124.7317 Evaluate side-chains 194 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 399 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 39 optimal weight: 0.0980 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.153961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.120344 restraints weight = 17833.647| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.71 r_work: 0.3122 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15196 Z= 0.159 Angle : 0.534 8.015 20608 Z= 0.278 Chirality : 0.041 0.142 2312 Planarity : 0.004 0.029 2540 Dihedral : 12.804 151.055 2120 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.86 % Allowed : 11.60 % Favored : 87.53 % 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: 0.75 (0.21), residues: 1792 helix: 1.11 (0.16), residues: 1068 sheet: -0.10 (0.70), residues: 56 loop : -0.33 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.018 0.001 TYR D 349 PHE 0.014 0.002 PHE C 389 TRP 0.020 0.002 TRP C 168 HIS 0.001 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (15196) covalent geometry : angle 0.53417 / 0.28 (20608) hydrogen bonds : bond 0.03966 / 2.57 ( 904) hydrogen bonds : angle 4.74508 / 3.42 ( 2652) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.395 Fit side-chains REVERT: A 266 ASN cc_start: 0.8075 (t0) cc_final: 0.7806 (t0) REVERT: A 341 GLU cc_start: 0.8126 (tp30) cc_final: 0.7834 (tp30) REVERT: A 428 LYS cc_start: 0.7872 (mtpt) cc_final: 0.7532 (mptt) REVERT: A 450 GLU cc_start: 0.6716 (pt0) cc_final: 0.6337 (pp20) REVERT: A 496 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7353 (mt0) REVERT: A 605 LYS cc_start: 0.6649 (ptmt) cc_final: 0.6273 (mptp) REVERT: B 266 ASN cc_start: 0.8093 (t0) cc_final: 0.7825 (t0) REVERT: B 407 ARG cc_start: 0.7887 (tpt170) cc_final: 0.7557 (tpm-80) REVERT: B 428 LYS cc_start: 0.7893 (mtpt) cc_final: 0.7567 (mptt) REVERT: B 450 GLU cc_start: 0.6691 (pt0) cc_final: 0.6326 (pp20) REVERT: B 496 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7356 (mt0) REVERT: B 605 LYS cc_start: 0.6685 (ptmt) cc_final: 0.6276 (mptp) REVERT: C 232 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7059 (mm-30) REVERT: C 266 ASN cc_start: 0.8050 (t0) cc_final: 0.7781 (t0) REVERT: C 407 ARG cc_start: 0.7876 (tpt170) cc_final: 0.7548 (tpm-80) REVERT: C 428 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7564 (mptt) REVERT: C 450 GLU cc_start: 0.6677 (pt0) cc_final: 0.6297 (pp20) REVERT: C 496 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7337 (mt0) REVERT: C 605 LYS cc_start: 0.6658 (ptmt) cc_final: 0.6261 (mptp) REVERT: D 266 ASN cc_start: 0.8024 (t0) cc_final: 0.7757 (t0) REVERT: D 407 ARG cc_start: 0.7871 (tpt170) cc_final: 0.7545 (tpm-80) REVERT: D 428 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7538 (mptt) REVERT: D 450 GLU cc_start: 0.6641 (pt0) cc_final: 0.6293 (pp20) REVERT: D 496 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7357 (mt0) REVERT: D 605 LYS cc_start: 0.6646 (ptmt) cc_final: 0.6279 (mptp) outliers start: 14 outliers final: 4 residues processed: 194 average time/residue: 0.5445 time to fit residues: 115.8784 Evaluate side-chains 172 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 168 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 399 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 419 GLN A 444 ASN B 395 ASN B 419 GLN B 444 ASN C 395 ASN C 419 GLN C 444 ASN D 395 ASN D 419 GLN D 444 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116092 restraints weight = 17908.771| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.72 r_work: 0.3057 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15196 Z= 0.214 Angle : 0.568 8.337 20608 Z= 0.296 Chirality : 0.043 0.144 2312 Planarity : 0.004 0.030 2540 Dihedral : 12.852 149.226 2120 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.54 % Allowed : 12.22 % Favored : 86.23 % 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: 0.64 (0.20), residues: 1792 helix: 0.98 (0.16), residues: 1068 sheet: 0.14 (0.68), residues: 56 loop : -0.32 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 462 TYR 0.020 0.002 TYR A 349 PHE 0.017 0.002 PHE A 389 TRP 0.022 0.002 TRP B 168 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (15196) covalent geometry : angle 0.56824 / 0.30 (20608) hydrogen bonds : bond 0.04157 / 2.69 ( 904) hydrogen bonds : angle 4.86010 / 3.50 ( 2652) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.559 Fit side-chains REVERT: A 232 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7111 (mm-30) REVERT: A 266 ASN cc_start: 0.7853 (t0) cc_final: 0.7640 (t0) REVERT: A 341 GLU cc_start: 0.7984 (tp30) cc_final: 0.7750 (tp30) REVERT: A 428 LYS cc_start: 0.7812 (mtpt) cc_final: 0.7517 (mptt) REVERT: A 450 GLU cc_start: 0.6731 (pt0) cc_final: 0.6380 (pp20) REVERT: A 496 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7276 (mt0) REVERT: A 605 LYS cc_start: 0.6774 (ptmt) cc_final: 0.6409 (mptp) REVERT: B 232 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 266 ASN cc_start: 0.7871 (t0) cc_final: 0.7658 (t0) REVERT: B 428 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7536 (mptt) REVERT: B 450 GLU cc_start: 0.6742 (pt0) cc_final: 0.6344 (pp20) REVERT: B 496 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7295 (mt0) REVERT: B 605 LYS cc_start: 0.6783 (ptmt) cc_final: 0.6421 (mptp) REVERT: C 232 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7131 (mm-30) REVERT: C 266 ASN cc_start: 0.7861 (t0) cc_final: 0.7649 (t0) REVERT: C 428 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7526 (mptt) REVERT: C 450 GLU cc_start: 0.6758 (pt0) cc_final: 0.6346 (pp20) REVERT: C 496 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7296 (mt0) REVERT: C 605 LYS cc_start: 0.6777 (ptmt) cc_final: 0.6409 (mptp) REVERT: D 232 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7127 (mm-30) REVERT: D 266 ASN cc_start: 0.7860 (t0) cc_final: 0.7651 (t0) REVERT: D 428 LYS cc_start: 0.7795 (mtpt) cc_final: 0.7509 (mptt) REVERT: D 450 GLU cc_start: 0.6716 (pt0) cc_final: 0.6316 (pp20) REVERT: D 496 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7304 (mt0) REVERT: D 605 LYS cc_start: 0.6790 (ptmt) cc_final: 0.6429 (mptp) outliers start: 25 outliers final: 10 residues processed: 186 average time/residue: 0.6085 time to fit residues: 122.9485 Evaluate side-chains 176 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 154 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119417 restraints weight = 17855.498| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.69 r_work: 0.3115 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15196 Z= 0.144 Angle : 0.521 7.735 20608 Z= 0.270 Chirality : 0.040 0.143 2312 Planarity : 0.004 0.026 2540 Dihedral : 12.701 148.782 2120 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.11 % Allowed : 13.77 % Favored : 85.12 % 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: 0.95 (0.20), residues: 1792 helix: 1.21 (0.16), residues: 1068 sheet: 0.02 (0.64), residues: 56 loop : -0.13 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 347 TYR 0.015 0.001 TYR A 349 PHE 0.010 0.001 PHE B 298 TRP 0.021 0.002 TRP B 168 HIS 0.001 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (15196) covalent geometry : angle 0.52056 / 0.27 (20608) hydrogen bonds : bond 0.03770 / 2.45 ( 904) hydrogen bonds : angle 4.64556 / 3.34 ( 2652) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.599 Fit side-chains REVERT: A 232 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7126 (mm-30) REVERT: A 266 ASN cc_start: 0.8033 (t0) cc_final: 0.7793 (t0) REVERT: A 341 GLU cc_start: 0.8115 (tp30) cc_final: 0.7843 (tp30) REVERT: A 428 LYS cc_start: 0.7864 (mtpt) cc_final: 0.7543 (mptt) REVERT: A 450 GLU cc_start: 0.6714 (pt0) cc_final: 0.6324 (pp20) REVERT: A 496 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7360 (mt0) REVERT: A 540 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7028 (m-30) REVERT: A 605 LYS cc_start: 0.6882 (ptmt) cc_final: 0.6478 (mptp) REVERT: B 232 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7124 (mm-30) REVERT: B 266 ASN cc_start: 0.8070 (t0) cc_final: 0.7826 (t0) REVERT: B 428 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7569 (mptt) REVERT: B 450 GLU cc_start: 0.6738 (pt0) cc_final: 0.6371 (pp20) REVERT: B 496 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7357 (mt0) REVERT: B 540 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: B 605 LYS cc_start: 0.6903 (ptmt) cc_final: 0.6491 (mptp) REVERT: C 232 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7120 (mm-30) REVERT: C 266 ASN cc_start: 0.8046 (t0) cc_final: 0.7805 (t0) REVERT: C 428 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7560 (mptt) REVERT: C 450 GLU cc_start: 0.6787 (pt0) cc_final: 0.6354 (pp20) REVERT: C 496 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7391 (mt0) REVERT: C 540 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: C 605 LYS cc_start: 0.6913 (ptmt) cc_final: 0.6491 (mptp) REVERT: D 232 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 266 ASN cc_start: 0.8029 (t0) cc_final: 0.7789 (t0) REVERT: D 428 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7544 (mptt) REVERT: D 450 GLU cc_start: 0.6773 (pt0) cc_final: 0.6354 (pp20) REVERT: D 496 GLN cc_start: 0.7744 (mm-40) cc_final: 0.7401 (mt0) REVERT: D 605 LYS cc_start: 0.6884 (ptmt) cc_final: 0.6477 (mptp) outliers start: 18 outliers final: 7 residues processed: 176 average time/residue: 0.5693 time to fit residues: 109.9571 Evaluate side-chains 171 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.156066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123656 restraints weight = 17737.637| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.73 r_work: 0.3174 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15196 Z= 0.114 Angle : 0.500 9.157 20608 Z= 0.256 Chirality : 0.040 0.143 2312 Planarity : 0.003 0.033 2540 Dihedral : 12.596 147.945 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.93 % Allowed : 14.57 % Favored : 84.51 % 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: 1.27 (0.20), residues: 1792 helix: 1.46 (0.16), residues: 1064 sheet: 0.67 (0.68), residues: 48 loop : -0.02 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.012 0.001 TYR B 199 PHE 0.009 0.001 PHE C 389 TRP 0.019 0.001 TRP B 168 HIS 0.001 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15196) covalent geometry : angle 0.50024 / 0.26 (20608) hydrogen bonds : bond 0.03529 / 2.31 ( 904) hydrogen bonds : angle 4.46981 / 3.20 ( 2652) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.514 Fit side-chains REVERT: A 232 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 266 ASN cc_start: 0.7956 (t0) cc_final: 0.7677 (t0) REVERT: A 428 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7517 (mptt) REVERT: A 450 GLU cc_start: 0.6632 (pt0) cc_final: 0.6299 (pp20) REVERT: A 496 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7325 (mt0) REVERT: A 540 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: A 605 LYS cc_start: 0.6752 (ptmt) cc_final: 0.6396 (mptp) REVERT: B 232 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6934 (mm-30) REVERT: B 266 ASN cc_start: 0.7938 (t0) cc_final: 0.7659 (t0) REVERT: B 428 LYS cc_start: 0.7792 (mtpt) cc_final: 0.7537 (mptt) REVERT: B 450 GLU cc_start: 0.6650 (pt0) cc_final: 0.6300 (pp20) REVERT: B 496 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7315 (mt0) REVERT: B 540 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: B 605 LYS cc_start: 0.6777 (ptmt) cc_final: 0.6408 (mptp) REVERT: C 232 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6910 (mm-30) REVERT: C 266 ASN cc_start: 0.7936 (t0) cc_final: 0.7660 (t0) REVERT: C 428 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7533 (mptt) REVERT: C 450 GLU cc_start: 0.6633 (pt0) cc_final: 0.6276 (pp20) REVERT: C 496 GLN cc_start: 0.7633 (mm-40) cc_final: 0.7318 (mt0) REVERT: C 540 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: C 605 LYS cc_start: 0.6756 (ptmt) cc_final: 0.6394 (mptp) REVERT: D 232 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6891 (mm-30) REVERT: D 266 ASN cc_start: 0.7897 (t0) cc_final: 0.7620 (t0) REVERT: D 428 LYS cc_start: 0.7774 (mtpt) cc_final: 0.7507 (mptt) REVERT: D 450 GLU cc_start: 0.6624 (pt0) cc_final: 0.6277 (pp20) REVERT: D 496 GLN cc_start: 0.7657 (mm-40) cc_final: 0.7329 (mt0) REVERT: D 540 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6845 (m-30) REVERT: D 605 LYS cc_start: 0.6747 (ptmt) cc_final: 0.6397 (mptp) outliers start: 15 outliers final: 11 residues processed: 170 average time/residue: 0.5715 time to fit residues: 106.3536 Evaluate side-chains 164 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 178 optimal weight: 0.0270 chunk 97 optimal weight: 5.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 419 GLN A 422 HIS B 395 ASN B 419 GLN B 422 HIS C 395 ASN C 419 GLN C 422 HIS D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.156198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.122627 restraints weight = 17796.809| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.71 r_work: 0.3163 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15196 Z= 0.116 Angle : 0.508 8.516 20608 Z= 0.259 Chirality : 0.040 0.147 2312 Planarity : 0.003 0.031 2540 Dihedral : 12.577 148.065 2120 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.79 % Allowed : 14.20 % Favored : 84.01 % 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: 1.36 (0.20), residues: 1792 helix: 1.52 (0.16), residues: 1064 sheet: 0.66 (0.68), residues: 48 loop : 0.04 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.015 0.001 TYR C 199 PHE 0.010 0.001 PHE B 535 TRP 0.018 0.001 TRP B 168 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (15196) covalent geometry : angle 0.50828 / 0.26 (20608) hydrogen bonds : bond 0.03472 / 2.27 ( 904) hydrogen bonds : angle 4.44552 / 3.19 ( 2652) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.586 Fit side-chains REVERT: A 232 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6998 (mm-30) REVERT: A 266 ASN cc_start: 0.7986 (t0) cc_final: 0.7704 (t0) REVERT: A 389 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.7977 (m-80) REVERT: A 428 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7486 (mptt) REVERT: A 450 GLU cc_start: 0.6676 (pt0) cc_final: 0.6309 (pp20) REVERT: A 496 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7367 (mt0) REVERT: A 605 LYS cc_start: 0.6757 (ptmt) cc_final: 0.6366 (mptp) REVERT: B 232 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 266 ASN cc_start: 0.7961 (t0) cc_final: 0.7683 (t0) REVERT: B 389 PHE cc_start: 0.8577 (OUTLIER) cc_final: 0.7978 (m-80) REVERT: B 450 GLU cc_start: 0.6614 (pt0) cc_final: 0.6281 (pp20) REVERT: B 496 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7356 (mt0) REVERT: B 605 LYS cc_start: 0.6791 (ptmt) cc_final: 0.6389 (mptp) REVERT: C 232 GLU cc_start: 0.7302 (mm-30) cc_final: 0.7027 (mm-30) REVERT: C 266 ASN cc_start: 0.7979 (t0) cc_final: 0.7694 (t0) REVERT: C 389 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7988 (m-80) REVERT: C 428 LYS cc_start: 0.7753 (mtpt) cc_final: 0.7527 (mptt) REVERT: C 450 GLU cc_start: 0.6637 (pt0) cc_final: 0.6285 (pp20) REVERT: C 496 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7358 (mt0) REVERT: C 605 LYS cc_start: 0.6756 (ptmt) cc_final: 0.6376 (mptp) REVERT: D 232 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7026 (mm-30) REVERT: D 266 ASN cc_start: 0.7946 (t0) cc_final: 0.7664 (t0) REVERT: D 389 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: D 428 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7481 (mptt) REVERT: D 450 GLU cc_start: 0.6571 (pt0) cc_final: 0.6252 (pp20) REVERT: D 496 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7376 (mt0) REVERT: D 605 LYS cc_start: 0.6786 (ptmt) cc_final: 0.6373 (mptp) outliers start: 29 outliers final: 16 residues processed: 181 average time/residue: 0.5550 time to fit residues: 110.2875 Evaluate side-chains 171 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 157 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 171 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 226 GLN A 245 GLN A 395 ASN A 419 GLN A 422 HIS B 245 GLN B 395 ASN B 419 GLN B 422 HIS C 226 GLN C 395 ASN C 419 GLN C 422 HIS D 226 GLN D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.118644 restraints weight = 17911.835| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.74 r_work: 0.3096 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15196 Z= 0.193 Angle : 0.558 8.218 20608 Z= 0.287 Chirality : 0.042 0.144 2312 Planarity : 0.004 0.064 2540 Dihedral : 12.706 147.119 2120 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.42 % Allowed : 15.74 % Favored : 82.84 % 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: 1.04 (0.20), residues: 1792 helix: 1.18 (0.15), residues: 1092 sheet: 0.50 (0.66), residues: 48 loop : 0.01 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.019 0.001 TYR A 349 PHE 0.015 0.002 PHE C 389 TRP 0.019 0.002 TRP C 168 HIS 0.002 0.001 HIS D 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (15196) covalent geometry : angle 0.55808 / 0.29 (20608) hydrogen bonds : bond 0.03910 / 2.53 ( 904) hydrogen bonds : angle 4.66759 / 3.35 ( 2652) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.416 Fit side-chains REVERT: A 232 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 266 ASN cc_start: 0.8075 (t0) cc_final: 0.7842 (t0) REVERT: A 389 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8364 (m-80) REVERT: A 395 ASN cc_start: 0.6994 (m-40) cc_final: 0.6392 (t0) REVERT: A 428 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7494 (mptt) REVERT: A 450 GLU cc_start: 0.6782 (pt0) cc_final: 0.6385 (pp20) REVERT: A 475 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7523 (ptpt) REVERT: A 496 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7416 (mt0) REVERT: A 605 LYS cc_start: 0.6960 (ptmt) cc_final: 0.6516 (mptp) REVERT: B 232 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7130 (mm-30) REVERT: B 266 ASN cc_start: 0.8111 (t0) cc_final: 0.7872 (t0) REVERT: B 389 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.8361 (m-80) REVERT: B 395 ASN cc_start: 0.6978 (m-40) cc_final: 0.6395 (t0) REVERT: B 450 GLU cc_start: 0.6773 (pt0) cc_final: 0.6392 (pp20) REVERT: B 475 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7547 (ptpt) REVERT: B 496 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7413 (mt0) REVERT: B 540 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: B 562 THR cc_start: 0.7925 (p) cc_final: 0.7644 (p) REVERT: B 605 LYS cc_start: 0.7015 (ptmt) cc_final: 0.6565 (mptp) REVERT: C 232 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7188 (mm-30) REVERT: C 266 ASN cc_start: 0.8100 (t0) cc_final: 0.7861 (t0) REVERT: C 389 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: C 395 ASN cc_start: 0.6976 (m-40) cc_final: 0.6382 (t0) REVERT: C 428 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7509 (mptt) REVERT: C 450 GLU cc_start: 0.6795 (pt0) cc_final: 0.6391 (pp20) REVERT: C 475 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7533 (ptpt) REVERT: C 496 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7428 (mt0) REVERT: C 540 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7201 (m-30) REVERT: C 605 LYS cc_start: 0.6992 (ptmt) cc_final: 0.6526 (mptp) REVERT: D 232 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7143 (mm-30) REVERT: D 266 ASN cc_start: 0.8062 (t0) cc_final: 0.7823 (t0) REVERT: D 389 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.8371 (m-80) REVERT: D 395 ASN cc_start: 0.7033 (m-40) cc_final: 0.6417 (t0) REVERT: D 428 LYS cc_start: 0.7766 (mtpt) cc_final: 0.7472 (mptt) REVERT: D 450 GLU cc_start: 0.6764 (pt0) cc_final: 0.6376 (pp20) REVERT: D 475 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7521 (ptpt) REVERT: D 496 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7450 (mt0) REVERT: D 605 LYS cc_start: 0.7001 (ptmt) cc_final: 0.6552 (mptp) outliers start: 23 outliers final: 14 residues processed: 170 average time/residue: 0.5323 time to fit residues: 99.2678 Evaluate side-chains 177 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 GLN A 422 HIS B 419 GLN C 419 GLN C 422 HIS D 419 GLN D 422 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121900 restraints weight = 17976.663| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.67 r_work: 0.3155 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15196 Z= 0.119 Angle : 0.511 8.359 20608 Z= 0.261 Chirality : 0.040 0.144 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.618 148.275 2120 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.30 % Allowed : 15.62 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1792 helix: 1.39 (0.16), residues: 1088 sheet: 0.58 (0.68), residues: 48 loop : 0.03 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 407 TYR 0.012 0.001 TYR A 349 PHE 0.012 0.001 PHE B 535 TRP 0.020 0.002 TRP D 168 HIS 0.001 0.000 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15196) covalent geometry : angle 0.51141 / 0.26 (20608) hydrogen bonds : bond 0.03560 / 2.33 ( 904) hydrogen bonds : angle 4.48545 / 3.22 ( 2652) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.597 Fit side-chains REVERT: A 232 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6951 (mm-30) REVERT: A 266 ASN cc_start: 0.7958 (t0) cc_final: 0.7707 (t0) REVERT: A 389 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8043 (m-80) REVERT: A 428 LYS cc_start: 0.7723 (mtpt) cc_final: 0.7490 (mptt) REVERT: A 450 GLU cc_start: 0.6724 (pt0) cc_final: 0.6296 (pp20) REVERT: A 496 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7366 (mt0) REVERT: A 540 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: A 605 LYS cc_start: 0.6770 (ptmt) cc_final: 0.6389 (mptp) REVERT: B 232 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 266 ASN cc_start: 0.7963 (t0) cc_final: 0.7705 (t0) REVERT: B 389 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8038 (m-80) REVERT: B 450 GLU cc_start: 0.6753 (pt0) cc_final: 0.6351 (pp20) REVERT: B 496 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7396 (mt0) REVERT: B 562 THR cc_start: 0.7946 (p) cc_final: 0.7707 (p) REVERT: B 605 LYS cc_start: 0.6820 (ptmt) cc_final: 0.6424 (mptp) REVERT: C 226 GLN cc_start: 0.7953 (mp10) cc_final: 0.7727 (tp40) REVERT: C 232 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6982 (mm-30) REVERT: C 266 ASN cc_start: 0.7963 (t0) cc_final: 0.7706 (t0) REVERT: C 389 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: C 450 GLU cc_start: 0.6725 (pt0) cc_final: 0.6315 (pp20) REVERT: C 496 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7378 (mt0) REVERT: C 540 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: C 605 LYS cc_start: 0.6815 (ptmt) cc_final: 0.6415 (mptp) REVERT: D 232 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6931 (mm-30) REVERT: D 266 ASN cc_start: 0.7910 (t0) cc_final: 0.7664 (t0) REVERT: D 389 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: D 428 LYS cc_start: 0.7716 (mtpt) cc_final: 0.7483 (mptt) REVERT: D 450 GLU cc_start: 0.6673 (pt0) cc_final: 0.6276 (pp20) REVERT: D 496 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7404 (mt0) REVERT: D 540 ASP cc_start: 0.7336 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: D 605 LYS cc_start: 0.6775 (ptmt) cc_final: 0.6398 (mptp) outliers start: 21 outliers final: 12 residues processed: 164 average time/residue: 0.5784 time to fit residues: 104.6509 Evaluate side-chains 167 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 402 ASN A 419 GLN A 422 HIS B 395 ASN B 402 ASN B 419 GLN B 422 HIS C 395 ASN C 402 ASN C 419 GLN C 422 HIS D 395 ASN D 402 ASN D 419 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.154824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122235 restraints weight = 17833.747| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.67 r_work: 0.3162 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15196 Z= 0.136 Angle : 0.520 8.561 20608 Z= 0.267 Chirality : 0.040 0.141 2312 Planarity : 0.004 0.028 2540 Dihedral : 12.624 148.152 2120 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.23 % Allowed : 16.30 % Favored : 82.47 % 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: 1.24 (0.20), residues: 1792 helix: 1.38 (0.15), residues: 1088 sheet: 0.55 (0.66), residues: 48 loop : 0.04 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.017 0.001 TYR B 199 PHE 0.012 0.001 PHE A 535 TRP 0.024 0.002 TRP A 442 HIS 0.002 0.001 HIS B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (15196) covalent geometry : angle 0.51983 / 0.27 (20608) hydrogen bonds : bond 0.03616 / 2.35 ( 904) hydrogen bonds : angle 4.52093 / 3.25 ( 2652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.426 Fit side-chains REVERT: A 232 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6919 (mm-30) REVERT: A 266 ASN cc_start: 0.7907 (t0) cc_final: 0.7655 (t0) REVERT: A 389 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.8220 (m-80) REVERT: A 450 GLU cc_start: 0.6736 (pt0) cc_final: 0.6315 (pp20) REVERT: A 496 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7331 (mt0) REVERT: A 605 LYS cc_start: 0.6873 (ptmt) cc_final: 0.6486 (mptp) REVERT: B 232 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6966 (mm-30) REVERT: B 266 ASN cc_start: 0.7908 (t0) cc_final: 0.7651 (t0) REVERT: B 389 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8213 (m-80) REVERT: B 450 GLU cc_start: 0.6702 (pt0) cc_final: 0.6300 (pp20) REVERT: B 496 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7334 (mt0) REVERT: B 562 THR cc_start: 0.7970 (p) cc_final: 0.7685 (p) REVERT: B 605 LYS cc_start: 0.6885 (ptmt) cc_final: 0.6495 (mptp) REVERT: C 226 GLN cc_start: 0.8104 (mp10) cc_final: 0.7734 (mm110) REVERT: C 232 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6960 (mm-30) REVERT: C 266 ASN cc_start: 0.7896 (t0) cc_final: 0.7638 (t0) REVERT: C 389 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: C 450 GLU cc_start: 0.6714 (pt0) cc_final: 0.6300 (pp20) REVERT: C 496 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7298 (mt0) REVERT: C 605 LYS cc_start: 0.6870 (ptmt) cc_final: 0.6512 (mptp) REVERT: D 232 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6952 (mm-30) REVERT: D 266 ASN cc_start: 0.7891 (t0) cc_final: 0.7610 (t0) REVERT: D 389 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8216 (m-80) REVERT: D 450 GLU cc_start: 0.6655 (pt0) cc_final: 0.6263 (pp20) REVERT: D 496 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7309 (mt0) REVERT: D 605 LYS cc_start: 0.6874 (ptmt) cc_final: 0.6501 (mptp) outliers start: 20 outliers final: 15 residues processed: 165 average time/residue: 0.5394 time to fit residues: 97.8187 Evaluate side-chains 173 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 143 optimal weight: 0.0770 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.122934 restraints weight = 17922.005| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.70 r_work: 0.3169 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15196 Z= 0.114 Angle : 0.503 8.142 20608 Z= 0.257 Chirality : 0.039 0.144 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.582 149.092 2120 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.17 % Allowed : 16.36 % Favored : 82.47 % 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: 1.38 (0.20), residues: 1792 helix: 1.49 (0.16), residues: 1088 sheet: 0.63 (0.67), residues: 48 loop : 0.08 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.015 0.001 TYR C 199 PHE 0.011 0.001 PHE A 535 TRP 0.021 0.001 TRP A 442 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (15196) covalent geometry : angle 0.50276 / 0.26 (20608) hydrogen bonds : bond 0.03448 / 2.25 ( 904) hydrogen bonds : angle 4.41450 / 3.17 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4143.10 seconds wall clock time: 71 minutes 41.76 seconds (4301.76 seconds total)