Starting phenix.real_space_refine on Wed Mar 4 15:48:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfx_23308/03_2026/7lfx_23308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfx_23308/03_2026/7lfx_23308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lfx_23308/03_2026/7lfx_23308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfx_23308/03_2026/7lfx_23308_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lfx_23308/03_2026/7lfx_23308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfx_23308/03_2026/7lfx_23308.map" } resolution = 3.1 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= 0.000 sd= 0.004 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-5986/lib/python3.9/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: 3.41, per 1000 atoms: 0.23 Number of scatterers: 14846 At special positions: 0 Unit cell: (94.185, 94.185, 115.115, 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: 1.35 Conformation dependent library (CDL) restraints added in 372.6 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: 0.45 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: 3.828A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.536A 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: 3.524A 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: 4.237A 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: 3.642A 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: 3.524A 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: 4.461A 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: 3.536A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.586A 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: 3.769A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.733A 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: 3.524A 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: 4.236A 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: 3.642A 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: 4.907A 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: 3.524A 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: 4.237A pdb=" N GLU D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 4.462A 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: 7.058A 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: 4.723A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.673A 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: 6.495A 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: 7.058A 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: 4.723A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.673A 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: 7.057A 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: 7.861A 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: 6.493A 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: 7.057A 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: 7.861A 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: 7.058A 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: 4.724A 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: 6.495A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 7.058A 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: 4.724A 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: 7.059A 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: 7.859A 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: 7.059A 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: 7.859A 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: 2.81 Time building geometry restraints manager: 1.86 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: 4304 1.34 - 1.45: 2412 1.45 - 1.57: 8344 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 1.478 0.104 2.00e-02 2.50e+03 2.71e+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 2.71e+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 2.71e+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 2.70e+01 bond pdb=" C1' PCG D 701 " pdb=" O4' PCG D 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 - 1.85: 20207 1.85 - 3.71: 282 3.71 - 5.56: 71 5.56 - 7.42: 24 7.42 - 9.27: 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 112.89 119.23 -6.34 1.24e+00 6.50e-01 2.61e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.20 -6.31 1.24e+00 6.50e-01 2.59e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.17 -6.28 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 100.83 110.10 -9.27 3.00e+00 1.11e-01 9.56e+00 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 8794 28.99 - 57.98: 286 57.98 - 86.97: 8 86.97 - 115.96: 4 115.96 - 144.95: 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 -63.64 -144.95 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG A 701 " pdb=" O3' PCG A 701 " pdb=" PA PCG A 701 " pdb=" O1A PCG A 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.66 -144.93 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 -63.66 -144.93 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 - 0.262: 28 0.262 - 0.392: 4 0.392 - 0.523: 0 0.523 - 0.654: 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 -3.35 -0.65 2.00e-01 2.50e+01 1.07e+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 1.55e-02 2.39e+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 2.37e+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 A 526 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.31e+00 pdb=" C VAL A 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL A 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2635 2.76 - 3.30: 15662 3.30 - 3.83: 26894 3.83 - 4.37: 32518 4.37 - 4.90: 53443 Nonbonded interactions: 131152 Sorted by model distance: nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 3.040 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 2.227 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.227 3.040 nonbonded pdb=" O THR D 357 " pdb=" OG1 THR D 361 " model vdw 2.319 3.040 ... (remaining 131147 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: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.260 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.104 15196 Z= 0.231 Angle : 0.697 9.274 20608 Z= 0.370 Chirality : 0.052 0.654 2312 Planarity : 0.003 0.028 2540 Dihedral : 14.964 144.946 5696 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.25 % Allowed : 2.65 % Favored : 97.10 % 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: -1.27 (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 0.015 0.001 TYR A 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 covalent geometry : bond 0.00482 (15196) covalent geometry : angle 0.69657 (20608) hydrogen bonds : bond 0.12174 ( 904) hydrogen bonds : angle 6.69147 ( 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 370 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 366 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8512 (mt) cc_final: 0.8307 (mt) REVERT: A 594 MET cc_start: 0.4708 (ppp) cc_final: 0.3440 (ttt) REVERT: B 387 LEU cc_start: 0.8518 (mt) cc_final: 0.8311 (mt) REVERT: B 594 MET cc_start: 0.4704 (ppp) cc_final: 0.3432 (ttt) REVERT: C 220 ARG cc_start: 0.7772 (mmt90) cc_final: 0.7463 (mmt90) REVERT: C 387 LEU cc_start: 0.8528 (mt) cc_final: 0.8322 (mt) REVERT: C 594 MET cc_start: 0.4702 (ppp) cc_final: 0.3429 (ttt) REVERT: D 387 LEU cc_start: 0.8510 (mt) cc_final: 0.8305 (mt) REVERT: D 407 ARG cc_start: 0.7295 (ttt90) cc_final: 0.7031 (tpt170) REVERT: D 594 MET cc_start: 0.4692 (ppp) cc_final: 0.3433 (ttt) outliers start: 4 outliers final: 0 residues processed: 370 average time/residue: 0.1253 time to fit residues: 66.0569 Evaluate side-chains 214 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 302 ASN A 395 ASN A 422 HIS A 468 ASN A 496 GLN A 534 GLN B 238 ASN B 302 ASN B 395 ASN B 422 HIS B 444 ASN B 468 ASN B 496 GLN B 534 GLN C 238 ASN C 302 ASN C 395 ASN C 422 HIS C 468 ASN C 496 GLN C 534 GLN D 238 ASN D 302 ASN D 395 ASN D 411 GLN D 422 HIS D 444 ASN D 468 ASN D 496 GLN D 534 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.121728 restraints weight = 18541.671| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.66 r_work: 0.3300 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15196 Z= 0.129 Angle : 0.519 6.170 20608 Z= 0.276 Chirality : 0.040 0.146 2312 Planarity : 0.004 0.036 2540 Dihedral : 12.763 148.979 2120 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.35 % Allowed : 10.06 % Favored : 87.59 % 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: 0.25 (0.21), residues: 1792 helix: 0.74 (0.16), residues: 1092 sheet: -0.71 (0.65), residues: 56 loop : -0.61 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 413 TYR 0.011 0.001 TYR D 349 PHE 0.010 0.001 PHE C 574 TRP 0.017 0.002 TRP C 168 HIS 0.004 0.001 HIS C 422 Details of bonding type rmsd covalent geometry : bond 0.00283 (15196) covalent geometry : angle 0.51892 (20608) hydrogen bonds : bond 0.03957 ( 904) hydrogen bonds : angle 4.88813 ( 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 294 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7791 (m-30) cc_final: 0.7552 (m-30) REVERT: A 395 ASN cc_start: 0.7124 (m-40) cc_final: 0.6532 (t0) REVERT: A 498 GLN cc_start: 0.7653 (mt0) cc_final: 0.7327 (mt0) REVERT: A 594 MET cc_start: 0.5266 (ppp) cc_final: 0.3562 (ttt) REVERT: B 204 ASP cc_start: 0.7768 (m-30) cc_final: 0.7532 (m-30) REVERT: B 395 ASN cc_start: 0.7169 (m-40) cc_final: 0.6592 (t0) REVERT: B 450 GLU cc_start: 0.6655 (pt0) cc_final: 0.6361 (pm20) REVERT: B 498 GLN cc_start: 0.7676 (mt0) cc_final: 0.7354 (mt0) REVERT: B 594 MET cc_start: 0.5308 (ppp) cc_final: 0.3479 (ttt) REVERT: C 204 ASP cc_start: 0.7804 (m-30) cc_final: 0.7573 (m-30) REVERT: C 395 ASN cc_start: 0.7168 (m-40) cc_final: 0.6594 (t0) REVERT: C 464 GLU cc_start: 0.7062 (tp30) cc_final: 0.6700 (tt0) REVERT: C 498 GLN cc_start: 0.7628 (mt0) cc_final: 0.7316 (mt0) REVERT: C 594 MET cc_start: 0.5296 (ppp) cc_final: 0.3460 (ttt) REVERT: D 204 ASP cc_start: 0.7788 (m-30) cc_final: 0.7556 (m-30) REVERT: D 395 ASN cc_start: 0.7132 (m-40) cc_final: 0.6560 (t0) REVERT: D 464 GLU cc_start: 0.7075 (tp30) cc_final: 0.6753 (tt0) REVERT: D 498 GLN cc_start: 0.7652 (mt0) cc_final: 0.7326 (mt0) REVERT: D 594 MET cc_start: 0.5250 (ppp) cc_final: 0.3533 (ttt) outliers start: 38 outliers final: 14 residues processed: 278 average time/residue: 0.1080 time to fit residues: 45.1026 Evaluate side-chains 214 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 336 ASP Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 336 ASP Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 336 ASP Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 149 optimal weight: 0.4980 chunk 82 optimal weight: 0.0470 chunk 72 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 ASN B 444 ASN C 338 ASN D 444 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.156318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119209 restraints weight = 18582.510| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.73 r_work: 0.3238 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15196 Z= 0.125 Angle : 0.490 4.907 20608 Z= 0.262 Chirality : 0.040 0.159 2312 Planarity : 0.004 0.031 2540 Dihedral : 12.595 149.342 2120 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.48 % Allowed : 13.95 % Favored : 84.57 % 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: 1.05 (0.21), residues: 1792 helix: 1.32 (0.16), residues: 1060 sheet: 0.16 (0.68), residues: 56 loop : -0.13 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 433 TYR 0.009 0.001 TYR B 375 PHE 0.010 0.001 PHE A 298 TRP 0.016 0.001 TRP C 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00267 (15196) covalent geometry : angle 0.49020 (20608) hydrogen bonds : bond 0.03721 ( 904) hydrogen bonds : angle 4.54494 ( 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 253 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7719 (m-30) cc_final: 0.7072 (m-30) REVERT: A 205 TYR cc_start: 0.6058 (m-10) cc_final: 0.5532 (t80) REVERT: A 450 GLU cc_start: 0.6701 (pt0) cc_final: 0.6399 (pm20) REVERT: A 464 GLU cc_start: 0.7752 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 498 GLN cc_start: 0.7936 (mt0) cc_final: 0.7595 (mt0) REVERT: A 594 MET cc_start: 0.5297 (ppp) cc_final: 0.4001 (tpt) REVERT: B 204 ASP cc_start: 0.7715 (m-30) cc_final: 0.7068 (m-30) REVERT: B 205 TYR cc_start: 0.6045 (m-10) cc_final: 0.5530 (t80) REVERT: B 286 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7450 (mt0) REVERT: B 429 ASP cc_start: 0.8273 (t70) cc_final: 0.7994 (t70) REVERT: B 450 GLU cc_start: 0.6726 (pt0) cc_final: 0.6418 (pm20) REVERT: B 498 GLN cc_start: 0.7975 (mt0) cc_final: 0.7633 (mt0) REVERT: B 594 MET cc_start: 0.5267 (ppp) cc_final: 0.4003 (tpt) REVERT: C 204 ASP cc_start: 0.7724 (m-30) cc_final: 0.6989 (m-30) REVERT: C 205 TYR cc_start: 0.5499 (m-10) cc_final: 0.5220 (t80) REVERT: C 286 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7466 (mt0) REVERT: C 450 GLU cc_start: 0.6712 (pt0) cc_final: 0.6441 (pm20) REVERT: C 498 GLN cc_start: 0.7927 (mt0) cc_final: 0.7588 (mt0) REVERT: C 594 MET cc_start: 0.5250 (ppp) cc_final: 0.3978 (tpt) REVERT: D 204 ASP cc_start: 0.7704 (m-30) cc_final: 0.7057 (m-30) REVERT: D 205 TYR cc_start: 0.5493 (m-10) cc_final: 0.5203 (t80) REVERT: D 286 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7471 (mt0) REVERT: D 429 ASP cc_start: 0.8322 (t70) cc_final: 0.8056 (t70) REVERT: D 430 MET cc_start: 0.7990 (tpp) cc_final: 0.7418 (tpp) REVERT: D 450 GLU cc_start: 0.6747 (pt0) cc_final: 0.6448 (pm20) REVERT: D 498 GLN cc_start: 0.7918 (mt0) cc_final: 0.7582 (mt0) REVERT: D 594 MET cc_start: 0.5272 (ppp) cc_final: 0.3982 (tpt) outliers start: 24 outliers final: 11 residues processed: 241 average time/residue: 0.1057 time to fit residues: 39.1270 Evaluate side-chains 222 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 44 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN A 468 ASN A 564 ASN C 468 ASN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.153344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116062 restraints weight = 18546.865| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.71 r_work: 0.3272 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15196 Z= 0.128 Angle : 0.487 6.726 20608 Z= 0.258 Chirality : 0.040 0.150 2312 Planarity : 0.004 0.028 2540 Dihedral : 12.585 151.401 2120 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.98 % Allowed : 14.44 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.21), residues: 1792 helix: 1.38 (0.16), residues: 1060 sheet: 0.14 (0.62), residues: 56 loop : -0.07 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 433 TYR 0.010 0.001 TYR A 349 PHE 0.011 0.001 PHE B 298 TRP 0.017 0.001 TRP B 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00293 (15196) covalent geometry : angle 0.48663 (20608) hydrogen bonds : bond 0.03728 ( 904) hydrogen bonds : angle 4.50393 ( 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 260 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7728 (m-30) cc_final: 0.7117 (m-30) REVERT: A 286 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7531 (mt0) REVERT: A 407 ARG cc_start: 0.8227 (tpt170) cc_final: 0.8015 (tpt90) REVERT: A 450 GLU cc_start: 0.6754 (pt0) cc_final: 0.6528 (pm20) REVERT: A 498 GLN cc_start: 0.8112 (mt0) cc_final: 0.7891 (mt0) REVERT: A 594 MET cc_start: 0.5295 (ppp) cc_final: 0.4067 (tpt) REVERT: B 204 ASP cc_start: 0.7692 (m-30) cc_final: 0.7111 (m-30) REVERT: B 286 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7431 (mt0) REVERT: B 430 MET cc_start: 0.8556 (tpp) cc_final: 0.8225 (tpt) REVERT: B 450 GLU cc_start: 0.6764 (pt0) cc_final: 0.6552 (pm20) REVERT: B 498 GLN cc_start: 0.8151 (mt0) cc_final: 0.7908 (mt0) REVERT: B 594 MET cc_start: 0.5327 (ppp) cc_final: 0.4104 (tpt) REVERT: C 204 ASP cc_start: 0.7659 (m-30) cc_final: 0.7049 (m-30) REVERT: C 286 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7508 (mt0) REVERT: C 430 MET cc_start: 0.8541 (tpp) cc_final: 0.8226 (tpt) REVERT: C 450 GLU cc_start: 0.6745 (pt0) cc_final: 0.6507 (pm20) REVERT: C 498 GLN cc_start: 0.8137 (mt0) cc_final: 0.7903 (mt0) REVERT: C 594 MET cc_start: 0.5312 (ppp) cc_final: 0.4089 (tpt) REVERT: D 204 ASP cc_start: 0.7707 (m-30) cc_final: 0.7087 (m-30) REVERT: D 286 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7519 (mt0) REVERT: D 429 ASP cc_start: 0.8254 (t70) cc_final: 0.7923 (t70) REVERT: D 450 GLU cc_start: 0.6764 (pt0) cc_final: 0.6537 (pm20) REVERT: D 498 GLN cc_start: 0.8111 (mt0) cc_final: 0.7877 (mt0) REVERT: D 594 MET cc_start: 0.5257 (ppp) cc_final: 0.4042 (tpt) outliers start: 32 outliers final: 15 residues processed: 245 average time/residue: 0.1064 time to fit residues: 39.6895 Evaluate side-chains 223 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 0.0470 chunk 85 optimal weight: 0.0000 overall best weight: 0.5886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 ASN D 411 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.154142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116971 restraints weight = 18448.346| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.68 r_work: 0.3290 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15196 Z= 0.113 Angle : 0.480 5.192 20608 Z= 0.253 Chirality : 0.040 0.151 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.520 150.942 2120 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.85 % Allowed : 15.37 % Favored : 82.78 % 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: 1.11 (0.20), residues: 1792 helix: 1.31 (0.16), residues: 1084 sheet: 0.18 (0.62), residues: 56 loop : -0.05 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 407 TYR 0.009 0.001 TYR B 375 PHE 0.009 0.001 PHE B 298 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00254 (15196) covalent geometry : angle 0.47962 (20608) hydrogen bonds : bond 0.03553 ( 904) hydrogen bonds : angle 4.40324 ( 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 268 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7695 (m-30) cc_final: 0.7130 (m-30) REVERT: A 286 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7728 (mt0) REVERT: A 594 MET cc_start: 0.5156 (ppp) cc_final: 0.4005 (tpt) REVERT: B 204 ASP cc_start: 0.7674 (m-30) cc_final: 0.7106 (m-30) REVERT: B 286 GLN cc_start: 0.7805 (tm-30) cc_final: 0.7460 (mt0) REVERT: B 498 GLN cc_start: 0.8148 (mt0) cc_final: 0.7944 (mt0) REVERT: B 547 ILE cc_start: 0.7288 (OUTLIER) cc_final: 0.6960 (mp) REVERT: B 594 MET cc_start: 0.5219 (ppp) cc_final: 0.4095 (tpt) REVERT: C 204 ASP cc_start: 0.7659 (m-30) cc_final: 0.7093 (m-30) REVERT: C 286 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7574 (mt0) REVERT: C 498 GLN cc_start: 0.8140 (mt0) cc_final: 0.7929 (mt0) REVERT: C 547 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6954 (mp) REVERT: C 594 MET cc_start: 0.5197 (ppp) cc_final: 0.4066 (tpt) REVERT: D 204 ASP cc_start: 0.7723 (m-30) cc_final: 0.7172 (m-30) REVERT: D 286 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7573 (mt0) REVERT: D 407 ARG cc_start: 0.8387 (tpt90) cc_final: 0.8087 (tpt170) REVERT: D 498 GLN cc_start: 0.8162 (mt0) cc_final: 0.7960 (mt0) REVERT: D 594 MET cc_start: 0.5130 (ppp) cc_final: 0.3998 (tpt) outliers start: 30 outliers final: 11 residues processed: 253 average time/residue: 0.1026 time to fit residues: 40.0432 Evaluate side-chains 207 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 155 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 127 optimal weight: 0.2980 chunk 31 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 ASN B 314 ASN C 314 ASN C 444 ASN C 468 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.149255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112707 restraints weight = 18266.551| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.60 r_work: 0.3151 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3987 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= 0.144 Angle : 0.508 7.394 20608 Z= 0.266 Chirality : 0.040 0.148 2312 Planarity : 0.004 0.032 2540 Dihedral : 12.593 151.822 2120 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.53 % Allowed : 15.31 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 1792 helix: 1.22 (0.15), residues: 1084 sheet: 0.01 (0.61), residues: 56 loop : -0.06 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 407 TYR 0.011 0.001 TYR B 351 PHE 0.012 0.001 PHE D 298 TRP 0.018 0.002 TRP D 168 HIS 0.003 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00332 (15196) covalent geometry : angle 0.50833 (20608) hydrogen bonds : bond 0.03816 ( 904) hydrogen bonds : angle 4.48230 ( 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 243 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7673 (m-30) cc_final: 0.7114 (m-30) REVERT: A 286 GLN cc_start: 0.8339 (tm-30) cc_final: 0.7490 (mt0) REVERT: A 450 GLU cc_start: 0.6953 (pt0) cc_final: 0.6502 (pp20) REVERT: A 543 TYR cc_start: 0.7092 (p90) cc_final: 0.6691 (p90) REVERT: A 556 LYS cc_start: 0.2717 (OUTLIER) cc_final: 0.1796 (tptt) REVERT: A 594 MET cc_start: 0.5339 (ppp) cc_final: 0.4167 (tpt) REVERT: B 204 ASP cc_start: 0.7642 (m-30) cc_final: 0.7081 (m-30) REVERT: B 286 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7358 (mt0) REVERT: B 450 GLU cc_start: 0.6964 (pt0) cc_final: 0.6526 (pp20) REVERT: B 498 GLN cc_start: 0.8179 (mt0) cc_final: 0.7961 (mt0) REVERT: B 509 LYS cc_start: 0.6116 (mttt) cc_final: 0.5743 (mtpp) REVERT: B 556 LYS cc_start: 0.2649 (OUTLIER) cc_final: 0.1764 (tptt) REVERT: B 594 MET cc_start: 0.5387 (ppp) cc_final: 0.4234 (tpt) REVERT: C 204 ASP cc_start: 0.7635 (m-30) cc_final: 0.7052 (m-30) REVERT: C 286 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7457 (mt0) REVERT: C 306 TYR cc_start: 0.8382 (m-10) cc_final: 0.8173 (m-10) REVERT: C 498 GLN cc_start: 0.8164 (mt0) cc_final: 0.7960 (mt0) REVERT: C 556 LYS cc_start: 0.2610 (OUTLIER) cc_final: 0.1736 (tptt) REVERT: C 594 MET cc_start: 0.5370 (ppp) cc_final: 0.4222 (tpt) REVERT: D 204 ASP cc_start: 0.7662 (m-30) cc_final: 0.7094 (m-30) REVERT: D 286 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7447 (mt0) REVERT: D 306 TYR cc_start: 0.8370 (m-10) cc_final: 0.8169 (m-10) REVERT: D 494 LYS cc_start: 0.7817 (mppt) cc_final: 0.7602 (mppt) REVERT: D 498 GLN cc_start: 0.8202 (mt0) cc_final: 0.7975 (mt0) REVERT: D 543 TYR cc_start: 0.7114 (p90) cc_final: 0.6724 (p90) REVERT: D 556 LYS cc_start: 0.2708 (OUTLIER) cc_final: 0.1789 (tptt) REVERT: D 594 MET cc_start: 0.5300 (ppp) cc_final: 0.4109 (tpt) outliers start: 41 outliers final: 25 residues processed: 228 average time/residue: 0.1009 time to fit residues: 35.6438 Evaluate side-chains 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 0.7980 chunk 176 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 0.0070 chunk 95 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 468 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.151780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.115090 restraints weight = 18239.238| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.68 r_work: 0.3203 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15196 Z= 0.115 Angle : 0.487 7.040 20608 Z= 0.253 Chirality : 0.040 0.153 2312 Planarity : 0.003 0.032 2540 Dihedral : 12.491 149.510 2120 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 17.16 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.20), residues: 1792 helix: 1.35 (0.15), residues: 1084 sheet: -0.03 (0.61), residues: 56 loop : 0.03 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 407 TYR 0.009 0.001 TYR C 456 PHE 0.009 0.001 PHE A 298 TRP 0.018 0.001 TRP D 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00260 (15196) covalent geometry : angle 0.48670 (20608) hydrogen bonds : bond 0.03550 ( 904) hydrogen bonds : angle 4.36612 ( 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 230 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7669 (m-30) cc_final: 0.7095 (m-30) REVERT: A 286 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7526 (mt0) REVERT: A 306 TYR cc_start: 0.8383 (m-10) cc_final: 0.8170 (m-10) REVERT: A 450 GLU cc_start: 0.6977 (pt0) cc_final: 0.6535 (pp20) REVERT: A 543 TYR cc_start: 0.7082 (p90) cc_final: 0.6678 (p90) REVERT: A 594 MET cc_start: 0.5326 (ppp) cc_final: 0.4159 (tpt) REVERT: B 204 ASP cc_start: 0.7637 (m-30) cc_final: 0.7064 (m-30) REVERT: B 286 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7484 (mt0) REVERT: B 306 TYR cc_start: 0.8392 (m-10) cc_final: 0.8159 (m-10) REVERT: B 450 GLU cc_start: 0.7014 (pt0) cc_final: 0.6554 (pp20) REVERT: B 509 LYS cc_start: 0.6153 (mttt) cc_final: 0.5709 (mtpp) REVERT: B 543 TYR cc_start: 0.7098 (p90) cc_final: 0.6666 (p90) REVERT: B 594 MET cc_start: 0.5303 (ppp) cc_final: 0.4156 (tpt) REVERT: C 204 ASP cc_start: 0.7616 (m-30) cc_final: 0.7000 (m-30) REVERT: C 286 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7571 (mt0) REVERT: C 305 MET cc_start: 0.8123 (ttm) cc_final: 0.7884 (ttp) REVERT: C 306 TYR cc_start: 0.8421 (m-10) cc_final: 0.8217 (m-10) REVERT: C 543 TYR cc_start: 0.7073 (p90) cc_final: 0.6641 (p90) REVERT: C 594 MET cc_start: 0.5295 (ppp) cc_final: 0.4152 (tpt) REVERT: D 204 ASP cc_start: 0.7656 (m-30) cc_final: 0.7040 (m-30) REVERT: D 286 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7566 (mt0) REVERT: D 305 MET cc_start: 0.8106 (ttm) cc_final: 0.7865 (ttp) REVERT: D 306 TYR cc_start: 0.8405 (m-10) cc_final: 0.8204 (m-10) REVERT: D 509 LYS cc_start: 0.6144 (mttt) cc_final: 0.5695 (mtpp) REVERT: D 543 TYR cc_start: 0.7080 (p90) cc_final: 0.6693 (p90) REVERT: D 594 MET cc_start: 0.5323 (ppp) cc_final: 0.4152 (tpt) outliers start: 21 outliers final: 12 residues processed: 220 average time/residue: 0.1059 time to fit residues: 35.6929 Evaluate side-chains 199 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 157 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.0050 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.152954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.117258 restraints weight = 18138.494| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.62 r_work: 0.3179 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15196 Z= 0.128 Angle : 0.501 7.240 20608 Z= 0.260 Chirality : 0.040 0.153 2312 Planarity : 0.004 0.043 2540 Dihedral : 12.508 150.800 2120 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.04 % Allowed : 16.73 % Favored : 81.23 % 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: 1.13 (0.20), residues: 1792 helix: 1.35 (0.15), residues: 1084 sheet: -0.32 (0.60), residues: 56 loop : -0.05 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 407 TYR 0.009 0.001 TYR D 351 PHE 0.010 0.001 PHE D 298 TRP 0.017 0.001 TRP B 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00296 (15196) covalent geometry : angle 0.50095 (20608) hydrogen bonds : bond 0.03637 ( 904) hydrogen bonds : angle 4.39923 ( 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 239 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7595 (m-30) cc_final: 0.7070 (m-30) REVERT: A 286 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7624 (mt0) REVERT: A 297 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8184 (mm) REVERT: A 305 MET cc_start: 0.8128 (ttm) cc_final: 0.7921 (ttp) REVERT: A 331 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8591 (p) REVERT: A 430 MET cc_start: 0.8635 (tpp) cc_final: 0.8353 (tpt) REVERT: A 450 GLU cc_start: 0.7029 (pt0) cc_final: 0.6580 (pp20) REVERT: A 509 LYS cc_start: 0.6155 (mttt) cc_final: 0.5706 (mtpp) REVERT: A 543 TYR cc_start: 0.7116 (p90) cc_final: 0.6679 (p90) REVERT: A 556 LYS cc_start: 0.2400 (OUTLIER) cc_final: 0.2122 (mtmm) REVERT: A 594 MET cc_start: 0.5321 (ppp) cc_final: 0.4170 (tpt) REVERT: B 204 ASP cc_start: 0.7576 (m-30) cc_final: 0.7052 (m-30) REVERT: B 331 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8574 (p) REVERT: B 450 GLU cc_start: 0.7076 (pt0) cc_final: 0.6692 (pp20) REVERT: B 498 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: B 509 LYS cc_start: 0.6210 (mttt) cc_final: 0.5763 (mtpp) REVERT: B 543 TYR cc_start: 0.7146 (p90) cc_final: 0.6708 (p90) REVERT: B 556 LYS cc_start: 0.2443 (OUTLIER) cc_final: 0.1842 (mtmm) REVERT: B 594 MET cc_start: 0.5278 (ppp) cc_final: 0.4132 (tpt) REVERT: C 204 ASP cc_start: 0.7581 (m-30) cc_final: 0.7062 (m-30) REVERT: C 286 GLN cc_start: 0.7882 (tm-30) cc_final: 0.7542 (mt0) REVERT: C 305 MET cc_start: 0.8091 (ttm) cc_final: 0.7867 (ttp) REVERT: C 494 LYS cc_start: 0.7959 (mppt) cc_final: 0.7137 (mtmm) REVERT: C 498 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: C 509 LYS cc_start: 0.6148 (mttt) cc_final: 0.5749 (mtpp) REVERT: C 543 TYR cc_start: 0.7135 (p90) cc_final: 0.6698 (p90) REVERT: C 556 LYS cc_start: 0.2454 (OUTLIER) cc_final: 0.1849 (mtmm) REVERT: C 594 MET cc_start: 0.5292 (ppp) cc_final: 0.4137 (tpt) REVERT: D 204 ASP cc_start: 0.7604 (m-30) cc_final: 0.7077 (m-30) REVERT: D 286 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7531 (mt0) REVERT: D 305 MET cc_start: 0.8117 (ttm) cc_final: 0.7890 (ttp) REVERT: D 331 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8578 (p) REVERT: D 498 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: D 509 LYS cc_start: 0.6212 (mttt) cc_final: 0.5764 (mtpp) REVERT: D 543 TYR cc_start: 0.7130 (p90) cc_final: 0.6706 (p90) REVERT: D 556 LYS cc_start: 0.2380 (OUTLIER) cc_final: 0.2079 (mtmm) REVERT: D 594 MET cc_start: 0.5336 (ppp) cc_final: 0.4199 (tpt) outliers start: 33 outliers final: 13 residues processed: 227 average time/residue: 0.1053 time to fit residues: 36.5854 Evaluate side-chains 214 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 498 GLN Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 498 GLN Chi-restraints excluded: chain D residue 556 LYS Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.3980 chunk 85 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.150198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.114640 restraints weight = 18464.923| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.61 r_work: 0.3165 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4518 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= 0.133 Angle : 0.502 5.616 20608 Z= 0.261 Chirality : 0.040 0.148 2312 Planarity : 0.004 0.053 2540 Dihedral : 12.490 150.122 2120 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.85 % Allowed : 17.04 % Favored : 81.11 % 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: 1.05 (0.20), residues: 1792 helix: 1.32 (0.15), residues: 1084 sheet: -0.40 (0.61), residues: 56 loop : -0.14 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 407 TYR 0.010 0.001 TYR D 351 PHE 0.011 0.001 PHE C 298 TRP 0.018 0.002 TRP D 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00307 (15196) covalent geometry : angle 0.50213 (20608) hydrogen bonds : bond 0.03671 ( 904) hydrogen bonds : angle 4.43553 ( 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 236 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7550 (m-30) cc_final: 0.7047 (m-30) REVERT: A 286 GLN cc_start: 0.8161 (tm130) cc_final: 0.7604 (mt0) REVERT: A 297 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8141 (mm) REVERT: A 305 MET cc_start: 0.8092 (ttm) cc_final: 0.7861 (ttp) REVERT: A 331 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8549 (p) REVERT: A 430 MET cc_start: 0.8664 (tpp) cc_final: 0.8334 (tpt) REVERT: A 450 GLU cc_start: 0.7076 (pt0) cc_final: 0.6602 (pp20) REVERT: A 509 LYS cc_start: 0.6249 (mttt) cc_final: 0.5818 (mtpp) REVERT: A 543 TYR cc_start: 0.7183 (p90) cc_final: 0.6731 (p90) REVERT: A 594 MET cc_start: 0.5305 (ppp) cc_final: 0.4165 (tpt) REVERT: B 204 ASP cc_start: 0.7554 (m-30) cc_final: 0.7053 (m-30) REVERT: B 297 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8172 (mm) REVERT: B 303 LEU cc_start: 0.8747 (mt) cc_final: 0.8538 (mp) REVERT: B 331 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 450 GLU cc_start: 0.7121 (pt0) cc_final: 0.6716 (pp20) REVERT: B 498 GLN cc_start: 0.8307 (mt0) cc_final: 0.8099 (mt0) REVERT: B 509 LYS cc_start: 0.6309 (mttt) cc_final: 0.5889 (mtpp) REVERT: B 543 TYR cc_start: 0.7217 (p90) cc_final: 0.6750 (p90) REVERT: B 556 LYS cc_start: 0.2213 (OUTLIER) cc_final: 0.1618 (mtmm) REVERT: B 594 MET cc_start: 0.5153 (ppp) cc_final: 0.4179 (tpt) REVERT: C 204 ASP cc_start: 0.7561 (m-30) cc_final: 0.7044 (m-30) REVERT: C 286 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7444 (mt0) REVERT: C 297 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8183 (mm) REVERT: C 494 LYS cc_start: 0.7959 (mppt) cc_final: 0.7136 (mtmm) REVERT: C 498 GLN cc_start: 0.8271 (mt0) cc_final: 0.8066 (mt0) REVERT: C 509 LYS cc_start: 0.6279 (mttt) cc_final: 0.5851 (mtpp) REVERT: C 543 TYR cc_start: 0.7206 (p90) cc_final: 0.6733 (p90) REVERT: C 556 LYS cc_start: 0.2212 (OUTLIER) cc_final: 0.1613 (mtmm) REVERT: C 594 MET cc_start: 0.5142 (ppp) cc_final: 0.4158 (tpt) REVERT: D 204 ASP cc_start: 0.7565 (m-30) cc_final: 0.7049 (m-30) REVERT: D 286 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7430 (mt0) REVERT: D 297 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8168 (mm) REVERT: D 331 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8561 (p) REVERT: D 498 GLN cc_start: 0.8282 (mt0) cc_final: 0.8065 (mt0) REVERT: D 509 LYS cc_start: 0.6263 (mttt) cc_final: 0.5882 (mtpp) REVERT: D 543 TYR cc_start: 0.7202 (p90) cc_final: 0.6735 (p90) REVERT: D 594 MET cc_start: 0.5251 (ppp) cc_final: 0.4074 (tpt) outliers start: 30 outliers final: 14 residues processed: 225 average time/residue: 0.1014 time to fit residues: 35.3868 Evaluate side-chains 225 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 556 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 556 LYS Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 128 optimal weight: 0.1980 chunk 179 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.120130 restraints weight = 18186.299| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.61 r_work: 0.3219 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15196 Z= 0.110 Angle : 0.477 6.008 20608 Z= 0.250 Chirality : 0.039 0.148 2312 Planarity : 0.003 0.034 2540 Dihedral : 12.431 150.357 2120 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.17 % Allowed : 17.65 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1792 helix: 1.39 (0.16), residues: 1084 sheet: -0.27 (0.63), residues: 56 loop : -0.13 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 407 TYR 0.008 0.001 TYR C 165 PHE 0.009 0.001 PHE D 298 TRP 0.019 0.002 TRP D 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00251 (15196) covalent geometry : angle 0.47653 (20608) hydrogen bonds : bond 0.03455 ( 904) hydrogen bonds : angle 4.34828 ( 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 236 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 217 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7515 (m-30) cc_final: 0.7092 (m-30) REVERT: A 286 GLN cc_start: 0.8096 (tm130) cc_final: 0.7627 (mt0) REVERT: A 305 MET cc_start: 0.8064 (ttm) cc_final: 0.7785 (ttp) REVERT: A 331 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8487 (p) REVERT: A 450 GLU cc_start: 0.7033 (pt0) cc_final: 0.6561 (pp20) REVERT: A 509 LYS cc_start: 0.6191 (mttt) cc_final: 0.5770 (mtpp) REVERT: A 543 TYR cc_start: 0.7151 (p90) cc_final: 0.6704 (p90) REVERT: A 594 MET cc_start: 0.5231 (ppp) cc_final: 0.4057 (tpt) REVERT: B 204 ASP cc_start: 0.7513 (m-30) cc_final: 0.7087 (m-30) REVERT: B 305 MET cc_start: 0.8147 (ttm) cc_final: 0.7874 (ttp) REVERT: B 331 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8484 (p) REVERT: B 450 GLU cc_start: 0.7105 (pt0) cc_final: 0.6695 (pp20) REVERT: B 498 GLN cc_start: 0.8189 (mt0) cc_final: 0.7945 (mt0) REVERT: B 509 LYS cc_start: 0.6219 (mttt) cc_final: 0.5832 (mtpp) REVERT: B 543 TYR cc_start: 0.7193 (p90) cc_final: 0.6730 (p90) REVERT: B 594 MET cc_start: 0.5196 (ppp) cc_final: 0.4058 (tpt) REVERT: C 204 ASP cc_start: 0.7532 (m-30) cc_final: 0.7100 (m-30) REVERT: C 286 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7426 (mt0) REVERT: C 297 ILE cc_start: 0.8422 (mt) cc_final: 0.8091 (mm) REVERT: C 494 LYS cc_start: 0.7943 (mppt) cc_final: 0.7110 (mtmm) REVERT: C 509 LYS cc_start: 0.6258 (mttt) cc_final: 0.5830 (mtpp) REVERT: C 543 TYR cc_start: 0.7183 (p90) cc_final: 0.6725 (p90) REVERT: C 594 MET cc_start: 0.5096 (ppp) cc_final: 0.4107 (tpt) REVERT: D 204 ASP cc_start: 0.7534 (m-30) cc_final: 0.7108 (m-30) REVERT: D 286 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7411 (mt0) REVERT: D 297 ILE cc_start: 0.8396 (mt) cc_final: 0.8057 (mm) REVERT: D 331 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8506 (p) REVERT: D 498 GLN cc_start: 0.8153 (mt0) cc_final: 0.7928 (mt0) REVERT: D 509 LYS cc_start: 0.6110 (mttt) cc_final: 0.5756 (mtpp) REVERT: D 543 TYR cc_start: 0.7158 (p90) cc_final: 0.6714 (p90) REVERT: D 594 MET cc_start: 0.5243 (ppp) cc_final: 0.4072 (tpt) outliers start: 19 outliers final: 9 residues processed: 227 average time/residue: 0.0980 time to fit residues: 35.0322 Evaluate side-chains 220 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 575 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 575 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 114 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 143 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 152 optimal weight: 0.4980 chunk 125 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.154347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119556 restraints weight = 18206.051| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.62 r_work: 0.3210 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15196 Z= 0.114 Angle : 0.486 6.599 20608 Z= 0.252 Chirality : 0.039 0.151 2312 Planarity : 0.003 0.036 2540 Dihedral : 12.416 150.099 2120 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.30 % Allowed : 17.47 % Favored : 81.23 % 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: 1.14 (0.20), residues: 1792 helix: 1.41 (0.15), residues: 1084 sheet: -0.35 (0.63), residues: 56 loop : -0.13 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 407 TYR 0.008 0.001 TYR D 456 PHE 0.012 0.001 PHE C 389 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00260 (15196) covalent geometry : angle 0.48565 (20608) hydrogen bonds : bond 0.03505 ( 904) hydrogen bonds : angle 4.34461 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3428.02 seconds wall clock time: 59 minutes 38.73 seconds (3578.73 seconds total)