Starting phenix.real_space_refine on Fri Jul 3 14:49:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfx_23308/07_2026/7lfx_23308_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfx_23308/07_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_23308/07_2026/7lfx_23308_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfx_23308/07_2026/7lfx_23308_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lfx_23308/07_2026/7lfx_23308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfx_23308/07_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-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 23 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 3.14, per 1000 atoms: 0.21 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: 0.97 Conformation dependent library (CDL) restraints added in 449.7 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: 0.35 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: 2.36 Time building geometry restraints manager: 1.28 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.560 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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/Z covalent geometry : bond 0.00482 / 0.23 (15196) covalent geometry : angle 0.69657 / 0.37 (20608) hydrogen bonds : bond 0.12174 / 7.96 ( 904) hydrogen bonds : angle 6.69147 / 4.86 ( 2652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 366 time to evaluate : 0.539 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: 0.1174 time to fit residues: 62.2591 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 : 0.350 ------------------------------------------------------------------------------- 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... 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 338 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.157457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.121107 restraints weight = 18585.334| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.67 r_work: 0.3287 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2402 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= 0.131 Angle : 0.518 6.488 20608 Z= 0.276 Chirality : 0.040 0.146 2312 Planarity : 0.004 0.036 2540 Dihedral : 12.760 148.923 2120 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.22 % Allowed : 10.19 % 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: 0.26 (0.21), residues: 1792 helix: 0.74 (0.16), residues: 1092 sheet: -0.70 (0.65), residues: 56 loop : -0.60 (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 B 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (15196) covalent geometry : angle 0.51837 / 0.28 (20608) hydrogen bonds : bond 0.03954 / 2.57 ( 904) hydrogen bonds : angle 4.87830 / 3.52 ( 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 295 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 TYR cc_start: 0.5929 (m-10) cc_final: 0.5469 (t80) REVERT: A 395 ASN cc_start: 0.7119 (m-40) cc_final: 0.6523 (t0) REVERT: A 498 GLN cc_start: 0.7662 (mt0) cc_final: 0.7336 (mt0) REVERT: A 594 MET cc_start: 0.5263 (ppp) cc_final: 0.3557 (ttt) REVERT: B 204 ASP cc_start: 0.7758 (m-30) cc_final: 0.7525 (m-30) REVERT: B 395 ASN cc_start: 0.7166 (m-40) cc_final: 0.6586 (t0) REVERT: B 450 GLU cc_start: 0.6668 (pt0) cc_final: 0.6367 (pm20) REVERT: B 498 GLN cc_start: 0.7689 (mt0) cc_final: 0.7360 (mt0) REVERT: B 594 MET cc_start: 0.5309 (ppp) cc_final: 0.3480 (ttt) REVERT: C 204 ASP cc_start: 0.7803 (m-30) cc_final: 0.7573 (m-30) REVERT: C 464 GLU cc_start: 0.7054 (tp30) cc_final: 0.6721 (tt0) REVERT: C 498 GLN cc_start: 0.7643 (mt0) cc_final: 0.7324 (mt0) REVERT: C 594 MET cc_start: 0.5306 (ppp) cc_final: 0.3475 (ttt) REVERT: D 204 ASP cc_start: 0.7796 (m-30) cc_final: 0.7565 (m-30) REVERT: D 395 ASN cc_start: 0.7150 (m-40) cc_final: 0.6566 (t0) REVERT: D 464 GLU cc_start: 0.7045 (tp30) cc_final: 0.6728 (tt0) REVERT: D 498 GLN cc_start: 0.7668 (mt0) cc_final: 0.7339 (mt0) REVERT: D 594 MET cc_start: 0.5252 (ppp) cc_final: 0.3528 (ttt) outliers start: 36 outliers final: 12 residues processed: 281 average time/residue: 0.1079 time to fit residues: 45.9377 Evaluate side-chains 210 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 575 CYS 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: 5.9990 chunk 56 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 82 optimal weight: 0.0020 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 ASN B 444 ASN C 444 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 = 0.3769 r_free = 0.3769 target = 0.153836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116543 restraints weight = 18529.068| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.71 r_work: 0.3266 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15196 Z= 0.134 Angle : 0.502 4.683 20608 Z= 0.268 Chirality : 0.040 0.148 2312 Planarity : 0.004 0.032 2540 Dihedral : 12.625 149.498 2120 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.73 % Allowed : 13.46 % Favored : 84.81 % 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: 0.79 (0.21), residues: 1792 helix: 1.14 (0.16), residues: 1084 sheet: 0.09 (0.68), residues: 56 loop : -0.36 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 413 TYR 0.011 0.001 TYR A 349 PHE 0.011 0.001 PHE A 298 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15196) covalent geometry : angle 0.50194 / 0.27 (20608) hydrogen bonds : bond 0.03886 / 2.52 ( 904) hydrogen bonds : angle 4.60245 / 3.30 ( 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 246 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7767 (m-30) cc_final: 0.7120 (m-30) REVERT: A 205 TYR cc_start: 0.6149 (m-10) cc_final: 0.5646 (t80) REVERT: A 450 GLU cc_start: 0.6718 (pt0) cc_final: 0.6488 (pm20) REVERT: A 464 GLU cc_start: 0.7812 (tm-30) cc_final: 0.6856 (tm-30) REVERT: A 498 GLN cc_start: 0.7990 (mt0) cc_final: 0.7699 (mt0) REVERT: A 594 MET cc_start: 0.5293 (ppp) cc_final: 0.4028 (tpt) REVERT: B 204 ASP cc_start: 0.7742 (m-30) cc_final: 0.7098 (m-30) REVERT: B 205 TYR cc_start: 0.6113 (m-10) cc_final: 0.5629 (t80) REVERT: B 286 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7427 (mt0) REVERT: B 429 ASP cc_start: 0.8325 (t70) cc_final: 0.8071 (t70) REVERT: B 430 MET cc_start: 0.8393 (tpp) cc_final: 0.8167 (tpp) REVERT: B 450 GLU cc_start: 0.6724 (pt0) cc_final: 0.6504 (pm20) REVERT: B 498 GLN cc_start: 0.8034 (mt0) cc_final: 0.7732 (mt0) REVERT: B 594 MET cc_start: 0.5309 (ppp) cc_final: 0.4050 (tpt) REVERT: C 205 TYR cc_start: 0.5534 (m-10) cc_final: 0.5287 (t80) REVERT: C 286 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7503 (mt0) REVERT: C 429 ASP cc_start: 0.8290 (t70) cc_final: 0.8036 (t70) REVERT: C 430 MET cc_start: 0.8383 (tpp) cc_final: 0.8166 (tpp) REVERT: C 450 GLU cc_start: 0.6730 (pt0) cc_final: 0.6526 (pm20) REVERT: C 498 GLN cc_start: 0.7999 (mt0) cc_final: 0.7684 (mt0) REVERT: C 594 MET cc_start: 0.5248 (ppp) cc_final: 0.3983 (tpt) REVERT: D 204 ASP cc_start: 0.7771 (m-30) cc_final: 0.7129 (m-30) REVERT: D 205 TYR cc_start: 0.5556 (m-10) cc_final: 0.5294 (t80) REVERT: D 286 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7511 (mt0) REVERT: D 407 ARG cc_start: 0.8255 (tpt170) cc_final: 0.8034 (tpt170) REVERT: D 429 ASP cc_start: 0.8292 (t70) cc_final: 0.8044 (t70) REVERT: D 430 MET cc_start: 0.8037 (tpp) cc_final: 0.7458 (tpp) REVERT: D 498 GLN cc_start: 0.7967 (mt0) cc_final: 0.7678 (mt0) REVERT: D 594 MET cc_start: 0.5266 (ppp) cc_final: 0.4011 (tpt) outliers start: 28 outliers final: 16 residues processed: 238 average time/residue: 0.1085 time to fit residues: 39.1130 Evaluate side-chains 217 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 305 MET 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 305 MET 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 305 MET 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 575 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 129 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 155 optimal weight: 0.0040 chunk 61 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 ASN D 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.154018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116993 restraints weight = 18597.306| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.71 r_work: 0.3228 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3390 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= 0.117 Angle : 0.481 5.299 20608 Z= 0.254 Chirality : 0.040 0.150 2312 Planarity : 0.003 0.028 2540 Dihedral : 12.564 150.875 2120 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.79 % Allowed : 14.63 % 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: 1.13 (0.21), residues: 1792 helix: 1.37 (0.16), residues: 1060 sheet: 0.27 (0.63), residues: 56 loop : -0.09 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 407 TYR 0.009 0.001 TYR C 375 PHE 0.010 0.001 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (15196) covalent geometry : angle 0.48104 / 0.25 (20608) hydrogen bonds : bond 0.03607 / 2.36 ( 904) hydrogen bonds : angle 4.49164 / 3.21 ( 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 265 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7698 (m-30) cc_final: 0.7086 (m-30) REVERT: A 286 GLN cc_start: 0.8564 (tm-30) cc_final: 0.7679 (mt0) REVERT: A 450 GLU cc_start: 0.6748 (pt0) cc_final: 0.6505 (pm20) REVERT: A 464 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7012 (tp30) REVERT: A 498 GLN cc_start: 0.8154 (mt0) cc_final: 0.7924 (mt0) REVERT: A 547 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6888 (mp) REVERT: A 594 MET cc_start: 0.5311 (ppp) cc_final: 0.4073 (tpt) REVERT: B 204 ASP cc_start: 0.7676 (m-30) cc_final: 0.7121 (m-30) REVERT: B 286 GLN cc_start: 0.7811 (tm-30) cc_final: 0.7487 (mt0) REVERT: B 407 ARG cc_start: 0.8239 (tpt170) cc_final: 0.8020 (tpt90) REVERT: B 450 GLU cc_start: 0.6756 (pt0) cc_final: 0.6530 (pm20) REVERT: B 498 GLN cc_start: 0.8160 (mt0) cc_final: 0.7917 (mt0) REVERT: B 594 MET cc_start: 0.5386 (ppp) cc_final: 0.4163 (tpt) REVERT: C 204 ASP cc_start: 0.7644 (m-30) cc_final: 0.7027 (m-30) REVERT: C 286 GLN cc_start: 0.7885 (tm-30) cc_final: 0.7417 (mt0) REVERT: C 407 ARG cc_start: 0.8160 (tpt170) cc_final: 0.7917 (tpt90) REVERT: C 450 GLU cc_start: 0.6757 (pt0) cc_final: 0.6506 (pm20) REVERT: C 498 GLN cc_start: 0.8145 (mt0) cc_final: 0.7915 (mt0) REVERT: C 594 MET cc_start: 0.5346 (ppp) cc_final: 0.4121 (tpt) REVERT: D 204 ASP cc_start: 0.7698 (m-30) cc_final: 0.7086 (m-30) REVERT: D 286 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7419 (mt0) REVERT: D 430 MET cc_start: 0.8026 (tpp) cc_final: 0.7617 (tpp) REVERT: D 498 GLN cc_start: 0.8058 (mt0) cc_final: 0.7794 (mt0) REVERT: D 547 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6871 (mp) REVERT: D 594 MET cc_start: 0.5292 (ppp) cc_final: 0.4066 (tpt) outliers start: 29 outliers final: 12 residues processed: 253 average time/residue: 0.1005 time to fit residues: 38.4911 Evaluate side-chains 229 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 215 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 547 ILE 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 547 ILE 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: 4.9990 chunk 137 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 85 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.149672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112832 restraints weight = 18456.834| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.63 r_work: 0.3145 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3752 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= 0.145 Angle : 0.501 5.004 20608 Z= 0.265 Chirality : 0.041 0.150 2312 Planarity : 0.004 0.031 2540 Dihedral : 12.595 151.580 2120 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.65 % Allowed : 14.69 % Favored : 82.65 % 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: 0.96 (0.20), residues: 1792 helix: 1.18 (0.16), residues: 1084 sheet: 0.13 (0.60), residues: 56 loop : -0.10 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 407 TYR 0.011 0.001 TYR A 349 PHE 0.012 0.001 PHE A 298 TRP 0.018 0.002 TRP D 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (15196) covalent geometry : angle 0.50130 / 0.26 (20608) hydrogen bonds : bond 0.03821 / 2.49 ( 904) hydrogen bonds : angle 4.51968 / 3.23 ( 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 266 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7649 (m-30) cc_final: 0.7090 (m-30) REVERT: A 286 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7523 (mt0) REVERT: A 464 GLU cc_start: 0.7759 (tm-30) cc_final: 0.6864 (tp30) REVERT: A 498 GLN cc_start: 0.8177 (mt0) cc_final: 0.7875 (mt0) REVERT: A 556 LYS cc_start: 0.2743 (OUTLIER) cc_final: 0.1866 (tptt) REVERT: A 594 MET cc_start: 0.5297 (ppp) cc_final: 0.4077 (tpt) REVERT: B 204 ASP cc_start: 0.7648 (m-30) cc_final: 0.7081 (m-30) REVERT: B 286 GLN cc_start: 0.7824 (tm-30) cc_final: 0.7596 (mt0) REVERT: B 498 GLN cc_start: 0.8188 (mt0) cc_final: 0.7946 (mt0) REVERT: B 556 LYS cc_start: 0.2725 (OUTLIER) cc_final: 0.2301 (mptt) REVERT: B 594 MET cc_start: 0.5388 (ppp) cc_final: 0.4208 (tpt) REVERT: C 204 ASP cc_start: 0.7644 (m-30) cc_final: 0.7079 (m-30) REVERT: C 286 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7393 (mt0) REVERT: C 498 GLN cc_start: 0.8174 (mt0) cc_final: 0.7934 (mt0) REVERT: C 556 LYS cc_start: 0.2730 (OUTLIER) cc_final: 0.2293 (mptt) REVERT: C 594 MET cc_start: 0.5372 (ppp) cc_final: 0.4198 (tpt) REVERT: D 204 ASP cc_start: 0.7667 (m-30) cc_final: 0.7101 (m-30) REVERT: D 286 GLN cc_start: 0.7837 (tm-30) cc_final: 0.7463 (mt0) REVERT: D 407 ARG cc_start: 0.8263 (tpt170) cc_final: 0.8028 (tpt90) REVERT: D 430 MET cc_start: 0.8006 (tpp) cc_final: 0.7546 (tpp) REVERT: D 498 GLN cc_start: 0.8172 (mt0) cc_final: 0.7902 (mt0) REVERT: D 546 GLU cc_start: 0.6892 (pm20) cc_final: 0.6538 (pm20) REVERT: D 547 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6974 (mt) REVERT: D 556 LYS cc_start: 0.2735 (OUTLIER) cc_final: 0.2298 (mptt) REVERT: D 594 MET cc_start: 0.5271 (ppp) cc_final: 0.4066 (tpt) outliers start: 43 outliers final: 24 residues processed: 250 average time/residue: 0.0965 time to fit residues: 37.1853 Evaluate side-chains 229 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 331 THR Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 556 LYS 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: 0.0670 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 chunk 10 optimal weight: 0.0070 chunk 9 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 127 optimal weight: 0.0060 chunk 31 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.3352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN C 314 ASN D 314 ASN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.155694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120392 restraints weight = 18088.181| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.60 r_work: 0.3279 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15196 Z= 0.105 Angle : 0.469 5.464 20608 Z= 0.248 Chirality : 0.039 0.151 2312 Planarity : 0.003 0.033 2540 Dihedral : 12.507 150.886 2120 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.17 % Allowed : 16.91 % Favored : 81.91 % 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: 1.37 (0.16), residues: 1084 sheet: 0.29 (0.62), residues: 56 loop : -0.05 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 407 TYR 0.010 0.001 TYR D 456 PHE 0.007 0.001 PHE A 410 TRP 0.016 0.001 TRP D 168 HIS 0.003 0.001 HIS B 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (15196) covalent geometry : angle 0.46884 / 0.25 (20608) hydrogen bonds : bond 0.03430 / 2.25 ( 904) hydrogen bonds : angle 4.34558 / 3.10 ( 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 251 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7634 (m-30) cc_final: 0.7065 (m-30) REVERT: A 286 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7564 (mt0) REVERT: A 305 MET cc_start: 0.8068 (ttm) cc_final: 0.7841 (ttp) REVERT: A 306 TYR cc_start: 0.8306 (m-10) cc_final: 0.8076 (m-10) REVERT: A 430 MET cc_start: 0.8599 (tpp) cc_final: 0.8187 (tpp) REVERT: A 538 LEU cc_start: 0.7214 (mt) cc_final: 0.6993 (mt) REVERT: A 594 MET cc_start: 0.5248 (ppp) cc_final: 0.4070 (tpt) REVERT: B 204 ASP cc_start: 0.7607 (m-30) cc_final: 0.7030 (m-30) REVERT: B 305 MET cc_start: 0.8116 (ttm) cc_final: 0.7863 (ttp) REVERT: B 306 TYR cc_start: 0.8318 (m-10) cc_final: 0.8084 (m-10) REVERT: B 498 GLN cc_start: 0.8149 (mt0) cc_final: 0.7936 (mt0) REVERT: B 538 LEU cc_start: 0.7240 (mt) cc_final: 0.7024 (mt) REVERT: B 594 MET cc_start: 0.5241 (ppp) cc_final: 0.4079 (tpt) REVERT: C 204 ASP cc_start: 0.7595 (m-30) cc_final: 0.7033 (m-30) REVERT: C 286 GLN cc_start: 0.7720 (tm-30) cc_final: 0.7438 (mt0) REVERT: C 305 MET cc_start: 0.8066 (ttm) cc_final: 0.7811 (ttp) REVERT: C 306 TYR cc_start: 0.8318 (m-10) cc_final: 0.8075 (m-10) REVERT: C 538 LEU cc_start: 0.7224 (mt) cc_final: 0.7010 (mt) REVERT: C 594 MET cc_start: 0.5212 (ppp) cc_final: 0.4060 (tpt) REVERT: D 204 ASP cc_start: 0.7649 (m-30) cc_final: 0.7047 (m-30) REVERT: D 286 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7419 (mt0) REVERT: D 305 MET cc_start: 0.8056 (ttm) cc_final: 0.7801 (ttp) REVERT: D 306 TYR cc_start: 0.8323 (m-10) cc_final: 0.8083 (m-10) REVERT: D 407 ARG cc_start: 0.8244 (tpt170) cc_final: 0.7967 (tpt90) REVERT: D 498 GLN cc_start: 0.8066 (mt0) cc_final: 0.7827 (mt0) REVERT: D 538 LEU cc_start: 0.7190 (mt) cc_final: 0.6974 (mt) REVERT: D 594 MET cc_start: 0.5207 (ppp) cc_final: 0.4046 (tpt) outliers start: 19 outliers final: 12 residues processed: 239 average time/residue: 0.0891 time to fit residues: 33.2365 Evaluate side-chains 210 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 178 optimal weight: 4.9990 chunk 97 optimal weight: 0.0570 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.117507 restraints weight = 18296.048| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.60 r_work: 0.3204 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15196 Z= 0.108 Angle : 0.475 6.699 20608 Z= 0.248 Chirality : 0.039 0.150 2312 Planarity : 0.003 0.031 2540 Dihedral : 12.479 150.386 2120 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.17 % Allowed : 16.85 % Favored : 81.98 % 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: 1.21 (0.20), residues: 1792 helix: 1.47 (0.16), residues: 1080 sheet: 0.13 (0.61), residues: 56 loop : -0.14 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 424 TYR 0.008 0.001 TYR B 375 PHE 0.009 0.001 PHE A 298 TRP 0.016 0.001 TRP B 168 HIS 0.003 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (15196) covalent geometry : angle 0.47538 / 0.25 (20608) hydrogen bonds : bond 0.03432 / 2.25 ( 904) hydrogen bonds : angle 4.27861 / 3.05 ( 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 228 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 209 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7528 (m-30) cc_final: 0.7004 (m-30) REVERT: A 286 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7686 (mt0) REVERT: A 305 MET cc_start: 0.8111 (ttm) cc_final: 0.7890 (ttp) REVERT: A 331 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8568 (p) REVERT: A 430 MET cc_start: 0.8523 (tpp) cc_final: 0.8143 (tpp) REVERT: A 594 MET cc_start: 0.5318 (ppp) cc_final: 0.4126 (tpt) REVERT: B 204 ASP cc_start: 0.7508 (m-30) cc_final: 0.6980 (m-30) REVERT: B 305 MET cc_start: 0.8118 (ttm) cc_final: 0.7888 (ttp) REVERT: B 331 THR cc_start: 0.8793 (p) cc_final: 0.8572 (p) REVERT: B 498 GLN cc_start: 0.8183 (mt0) cc_final: 0.7974 (mt0) REVERT: B 594 MET cc_start: 0.5304 (ppp) cc_final: 0.4131 (tpt) REVERT: C 204 ASP cc_start: 0.7531 (m-30) cc_final: 0.6936 (m-30) REVERT: C 305 MET cc_start: 0.8081 (ttm) cc_final: 0.7850 (ttp) REVERT: C 331 THR cc_start: 0.8764 (p) cc_final: 0.8541 (p) REVERT: C 494 LYS cc_start: 0.7812 (mppt) cc_final: 0.7585 (mppt) REVERT: C 498 GLN cc_start: 0.8160 (mt0) cc_final: 0.7918 (mt0) REVERT: C 594 MET cc_start: 0.5298 (ppp) cc_final: 0.4120 (tpt) REVERT: D 204 ASP cc_start: 0.7526 (m-30) cc_final: 0.7000 (m-30) REVERT: D 286 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7437 (mt0) REVERT: D 305 MET cc_start: 0.8096 (ttm) cc_final: 0.7824 (ttp) REVERT: D 331 THR cc_start: 0.8795 (p) cc_final: 0.8574 (p) REVERT: D 407 ARG cc_start: 0.8260 (tpt170) cc_final: 0.7888 (tpt170) REVERT: D 498 GLN cc_start: 0.8076 (mt0) cc_final: 0.7809 (mt0) REVERT: D 594 MET cc_start: 0.5267 (ppp) cc_final: 0.4071 (tpt) outliers start: 19 outliers final: 8 residues processed: 222 average time/residue: 0.0927 time to fit residues: 32.0251 Evaluate side-chains 202 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 575 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 157 optimal weight: 0.5980 chunk 145 optimal weight: 0.0570 chunk 16 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN C 286 GLN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.154713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.119988 restraints weight = 18207.287| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.55 r_work: 0.3204 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15196 Z= 0.110 Angle : 0.475 7.257 20608 Z= 0.247 Chirality : 0.040 0.153 2312 Planarity : 0.003 0.038 2540 Dihedral : 12.444 150.146 2120 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.23 % Allowed : 17.22 % 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: 1.26 (0.20), residues: 1792 helix: 1.51 (0.16), residues: 1080 sheet: 0.03 (0.61), residues: 56 loop : -0.13 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.011 0.001 TYR B 456 PHE 0.010 0.001 PHE A 298 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15196) covalent geometry : angle 0.47473 / 0.25 (20608) hydrogen bonds : bond 0.03444 / 2.26 ( 904) hydrogen bonds : angle 4.26236 / 3.04 ( 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 229 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7506 (m-30) cc_final: 0.7089 (m-30) REVERT: A 286 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7674 (mt0) REVERT: A 303 LEU cc_start: 0.8680 (mt) cc_final: 0.8480 (mp) REVERT: A 331 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 430 MET cc_start: 0.8537 (tpp) cc_final: 0.8151 (tpp) REVERT: A 543 TYR cc_start: 0.7044 (p90) cc_final: 0.6645 (p90) REVERT: A 556 LYS cc_start: 0.2520 (OUTLIER) cc_final: 0.2229 (mtmm) REVERT: A 594 MET cc_start: 0.5273 (ppp) cc_final: 0.4127 (tpt) REVERT: B 204 ASP cc_start: 0.7453 (m-30) cc_final: 0.7034 (m-30) REVERT: B 303 LEU cc_start: 0.8727 (mt) cc_final: 0.8524 (mp) REVERT: B 305 MET cc_start: 0.8116 (ttm) cc_final: 0.7911 (ttp) REVERT: B 331 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8498 (p) REVERT: B 509 LYS cc_start: 0.6045 (mttt) cc_final: 0.5595 (mtpp) REVERT: B 543 TYR cc_start: 0.7061 (p90) cc_final: 0.6653 (p90) REVERT: B 556 LYS cc_start: 0.2451 (OUTLIER) cc_final: 0.2091 (mtmm) REVERT: B 594 MET cc_start: 0.5253 (ppp) cc_final: 0.4123 (tpt) REVERT: C 204 ASP cc_start: 0.7469 (m-30) cc_final: 0.7029 (m-30) REVERT: C 303 LEU cc_start: 0.8686 (mt) cc_final: 0.8481 (mp) REVERT: C 305 MET cc_start: 0.8053 (ttm) cc_final: 0.7845 (ttp) REVERT: C 331 THR cc_start: 0.8725 (p) cc_final: 0.8503 (p) REVERT: C 498 GLN cc_start: 0.8233 (mt0) cc_final: 0.8020 (mt0) REVERT: C 509 LYS cc_start: 0.6043 (mttt) cc_final: 0.5599 (mtpp) REVERT: C 543 TYR cc_start: 0.7054 (p90) cc_final: 0.6650 (p90) REVERT: C 556 LYS cc_start: 0.2493 (OUTLIER) cc_final: 0.2124 (mtmm) REVERT: C 594 MET cc_start: 0.5259 (ppp) cc_final: 0.4122 (tpt) REVERT: D 204 ASP cc_start: 0.7530 (m-30) cc_final: 0.7113 (m-30) REVERT: D 286 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7473 (mt0) REVERT: D 305 MET cc_start: 0.8035 (ttm) cc_final: 0.7816 (ttp) REVERT: D 331 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8495 (p) REVERT: D 407 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7880 (tpt170) REVERT: D 498 GLN cc_start: 0.8129 (mt0) cc_final: 0.7882 (mt0) REVERT: D 543 TYR cc_start: 0.6986 (p90) cc_final: 0.6598 (p90) REVERT: D 556 LYS cc_start: 0.2407 (OUTLIER) cc_final: 0.2062 (mtmm) REVERT: D 594 MET cc_start: 0.5220 (ppp) cc_final: 0.4070 (tpt) outliers start: 20 outliers final: 8 residues processed: 222 average time/residue: 0.0896 time to fit residues: 31.3868 Evaluate side-chains 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 556 LYS 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 556 LYS Chi-restraints excluded: chain B residue 575 CYS Chi-restraints excluded: chain C residue 197 LEU 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 331 THR 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: 0.7980 chunk 85 optimal weight: 0.5980 chunk 18 optimal weight: 0.3980 chunk 128 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 106 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN C 286 GLN ** D 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117449 restraints weight = 18480.592| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.62 r_work: 0.3202 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15196 Z= 0.109 Angle : 0.472 7.562 20608 Z= 0.246 Chirality : 0.039 0.153 2312 Planarity : 0.004 0.066 2540 Dihedral : 12.430 150.084 2120 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.42 % Allowed : 17.35 % 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: 1.29 (0.20), residues: 1792 helix: 1.55 (0.16), residues: 1080 sheet: -0.03 (0.62), residues: 56 loop : -0.14 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 407 TYR 0.010 0.001 TYR B 456 PHE 0.009 0.001 PHE A 298 TRP 0.016 0.001 TRP A 168 HIS 0.002 0.001 HIS D 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (15196) covalent geometry : angle 0.47234 / 0.25 (20608) hydrogen bonds : bond 0.03401 / 2.23 ( 904) hydrogen bonds : angle 4.26258 / 3.04 ( 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 246 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7628 (m-30) cc_final: 0.7119 (m-30) REVERT: A 286 GLN cc_start: 0.8324 (tm-30) cc_final: 0.7519 (mt0) REVERT: A 297 ILE cc_start: 0.8435 (mt) cc_final: 0.8102 (mm) REVERT: A 303 LEU cc_start: 0.8656 (mt) cc_final: 0.8444 (mp) REVERT: A 331 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8499 (p) REVERT: A 430 MET cc_start: 0.8560 (tpp) cc_final: 0.8157 (tpp) REVERT: A 509 LYS cc_start: 0.6052 (mttt) cc_final: 0.5658 (mtpp) REVERT: A 543 TYR cc_start: 0.7071 (p90) cc_final: 0.6667 (p90) REVERT: A 556 LYS cc_start: 0.2490 (OUTLIER) cc_final: 0.2243 (mtmm) REVERT: A 594 MET cc_start: 0.5291 (ppp) cc_final: 0.4121 (tpt) REVERT: B 204 ASP cc_start: 0.7581 (m-30) cc_final: 0.7075 (m-30) REVERT: B 297 ILE cc_start: 0.8386 (mt) cc_final: 0.8054 (mm) REVERT: B 303 LEU cc_start: 0.8662 (mt) cc_final: 0.8452 (mp) REVERT: B 305 MET cc_start: 0.8124 (ttm) cc_final: 0.7890 (ttp) REVERT: B 331 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 498 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: B 509 LYS cc_start: 0.6104 (mttt) cc_final: 0.5627 (mtpp) REVERT: B 543 TYR cc_start: 0.7081 (p90) cc_final: 0.6675 (p90) REVERT: B 556 LYS cc_start: 0.2451 (OUTLIER) cc_final: 0.2156 (mtmm) REVERT: B 594 MET cc_start: 0.5334 (ppp) cc_final: 0.4196 (tpt) REVERT: C 204 ASP cc_start: 0.7546 (m-30) cc_final: 0.7034 (m-30) REVERT: C 297 ILE cc_start: 0.8459 (mt) cc_final: 0.8123 (mm) REVERT: C 303 LEU cc_start: 0.8667 (mt) cc_final: 0.8458 (mp) REVERT: C 331 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8499 (p) REVERT: C 498 GLN cc_start: 0.8193 (mt0) cc_final: 0.7924 (mt0) REVERT: C 509 LYS cc_start: 0.6091 (mttt) cc_final: 0.5621 (mtpp) REVERT: C 543 TYR cc_start: 0.7083 (p90) cc_final: 0.6670 (p90) REVERT: C 556 LYS cc_start: 0.2451 (OUTLIER) cc_final: 0.2110 (mtmm) REVERT: C 594 MET cc_start: 0.5302 (ppp) cc_final: 0.4149 (tpt) REVERT: D 204 ASP cc_start: 0.7598 (m-30) cc_final: 0.7092 (m-30) REVERT: D 286 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7578 (mt0) REVERT: D 297 ILE cc_start: 0.8447 (mt) cc_final: 0.8110 (mm) REVERT: D 331 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8480 (p) REVERT: D 498 GLN cc_start: 0.8181 (mt0) cc_final: 0.7913 (mt0) REVERT: D 509 LYS cc_start: 0.6042 (mttt) cc_final: 0.5629 (mtpp) REVERT: D 543 TYR cc_start: 0.7013 (p90) cc_final: 0.6621 (p90) REVERT: D 556 LYS cc_start: 0.2289 (OUTLIER) cc_final: 0.2085 (mtmm) REVERT: D 594 MET cc_start: 0.5280 (ppp) cc_final: 0.4119 (tpt) outliers start: 23 outliers final: 9 residues processed: 237 average time/residue: 0.0966 time to fit residues: 36.1101 Evaluate side-chains 230 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU 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 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 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 331 THR Chi-restraints excluded: chain D residue 556 LYS 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: 10.0000 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 160 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN C 286 GLN ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 GLN D 468 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115226 restraints weight = 18417.385| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.62 r_work: 0.3169 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.4508 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= 0.123 Angle : 0.474 6.150 20608 Z= 0.250 Chirality : 0.040 0.150 2312 Planarity : 0.003 0.033 2540 Dihedral : 12.438 150.042 2120 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.54 % Allowed : 17.47 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.20), residues: 1792 helix: 1.51 (0.16), residues: 1084 sheet: -0.15 (0.62), residues: 56 loop : -0.11 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 433 TYR 0.010 0.001 TYR B 456 PHE 0.010 0.001 PHE A 298 TRP 0.016 0.001 TRP B 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15196) covalent geometry : angle 0.47435 / 0.25 (20608) hydrogen bonds : bond 0.03549 / 2.32 ( 904) hydrogen bonds : angle 4.31468 / 3.08 ( 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 244 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7610 (m-30) cc_final: 0.7101 (m-30) REVERT: A 286 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7618 (mt0) REVERT: A 297 ILE cc_start: 0.8431 (mt) cc_final: 0.8087 (mm) REVERT: A 331 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8497 (p) REVERT: A 430 MET cc_start: 0.8587 (tpp) cc_final: 0.8187 (tpp) REVERT: A 509 LYS cc_start: 0.6192 (mttt) cc_final: 0.5754 (mtpp) REVERT: A 543 TYR cc_start: 0.7173 (p90) cc_final: 0.6763 (p90) REVERT: A 594 MET cc_start: 0.5201 (ppp) cc_final: 0.4218 (tpt) REVERT: B 204 ASP cc_start: 0.7568 (m-30) cc_final: 0.7053 (m-30) REVERT: B 303 LEU cc_start: 0.8700 (mt) cc_final: 0.8491 (mp) REVERT: B 331 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8497 (p) REVERT: B 498 GLN cc_start: 0.8247 (mt0) cc_final: 0.8013 (mt0) REVERT: B 509 LYS cc_start: 0.6234 (mttt) cc_final: 0.5814 (mtpp) REVERT: B 543 TYR cc_start: 0.7166 (p90) cc_final: 0.6746 (p90) REVERT: B 594 MET cc_start: 0.5194 (ppp) cc_final: 0.4216 (tpt) REVERT: C 204 ASP cc_start: 0.7606 (m-30) cc_final: 0.7091 (m-30) REVERT: C 331 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8530 (p) REVERT: C 498 GLN cc_start: 0.8246 (mt0) cc_final: 0.8045 (mt0) REVERT: C 509 LYS cc_start: 0.6215 (mttt) cc_final: 0.5806 (mtpp) REVERT: C 543 TYR cc_start: 0.7178 (p90) cc_final: 0.6741 (p90) REVERT: C 594 MET cc_start: 0.5199 (ppp) cc_final: 0.4232 (tpt) REVERT: D 204 ASP cc_start: 0.7623 (m-30) cc_final: 0.7104 (m-30) REVERT: D 303 LEU cc_start: 0.8679 (mt) cc_final: 0.8462 (mp) REVERT: D 331 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8514 (p) REVERT: D 407 ARG cc_start: 0.8327 (tpt170) cc_final: 0.8108 (tpt170) REVERT: D 498 GLN cc_start: 0.8151 (mt0) cc_final: 0.7895 (mt0) REVERT: D 509 LYS cc_start: 0.6167 (mttt) cc_final: 0.5727 (mtpp) REVERT: D 543 TYR cc_start: 0.7122 (p90) cc_final: 0.6717 (p90) REVERT: D 594 MET cc_start: 0.5155 (ppp) cc_final: 0.4163 (tpt) outliers start: 25 outliers final: 12 residues processed: 233 average time/residue: 0.0921 time to fit residues: 33.9076 Evaluate side-chains 229 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 301 SER 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 225 GLU 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 301 SER 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: 0.7980 chunk 29 optimal weight: 1.9990 chunk 168 optimal weight: 0.0020 chunk 114 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 286 GLN ** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN D 468 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.118303 restraints weight = 18291.776| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.61 r_work: 0.3200 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15196 Z= 0.110 Angle : 0.474 6.736 20608 Z= 0.246 Chirality : 0.039 0.151 2312 Planarity : 0.003 0.032 2540 Dihedral : 12.407 149.921 2120 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.30 % Allowed : 17.78 % Favored : 80.93 % 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: 1.30 (0.20), residues: 1792 helix: 1.52 (0.16), residues: 1084 sheet: -0.10 (0.63), residues: 56 loop : -0.08 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 407 TYR 0.016 0.001 TYR D 456 PHE 0.009 0.001 PHE C 298 TRP 0.017 0.001 TRP A 168 HIS 0.002 0.001 HIS C 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (15196) covalent geometry : angle 0.47367 / 0.25 (20608) hydrogen bonds : bond 0.03418 / 2.24 ( 904) hydrogen bonds : angle 4.28653 / 3.06 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3318.00 seconds wall clock time: 57 minutes 51.39 seconds (3471.39 seconds total)