Starting phenix.real_space_refine on Wed Mar 4 15:54:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lfw_23307/03_2026/7lfw_23307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lfw_23307/03_2026/7lfw_23307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lfw_23307/03_2026/7lfw_23307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lfw_23307/03_2026/7lfw_23307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lfw_23307/03_2026/7lfw_23307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lfw_23307/03_2026/7lfw_23307.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 76 5.16 5 C 9684 2.51 5 N 2396 2.21 5 O 2684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14846 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3688 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 25 Unusual residues: {' CA': 2, 'PCG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PCG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.81, per 1000 atoms: 0.19 Number of scatterers: 14846 At special positions: 0 Unit cell: (96.485, 96.485, 114.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 76 16.00 P 4 15.00 O 2684 8.00 N 2396 7.00 C 9684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 533.8 milliseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 66.7% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 162 through 189 removed outlier: 3.523A pdb=" N TYR A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 5.259A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE A 202 " --> pdb=" O GLU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 242 Processing helix chain 'A' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE A 270 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.733A pdb=" N MET A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 290 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 326 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 Processing helix chain 'A' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 471 removed outlier: 5.039A pdb=" N GLU A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS A 605 " --> pdb=" O GLN A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Proline residue: B 175 - end of helix removed outlier: 5.261A pdb=" N ILE B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE B 202 " --> pdb=" O GLU B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 243 through 253 removed outlier: 3.840A pdb=" N LYS B 247 " --> pdb=" O ASN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 258 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 267 through 276 removed outlier: 3.769A pdb=" N ILE B 270 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASN B 273 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET B 281 " --> pdb=" O ARG B 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 290 " --> pdb=" O GLN B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 326 Processing helix chain 'B' and resid 344 through 361 Processing helix chain 'B' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY B 397 " --> pdb=" O VAL B 393 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ALA B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG B 407 " --> pdb=" O MET B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 444 Processing helix chain 'B' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU B 464 " --> pdb=" O LYS B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR C 166 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 5.253A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 removed outlier: 3.535A pdb=" N TYR C 196 " --> pdb=" O LEU C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE C 202 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 242 Processing helix chain 'C' and resid 243 through 253 removed outlier: 3.839A pdb=" N LYS C 247 " --> pdb=" O ASN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 258 Processing helix chain 'C' and resid 259 through 264 Processing helix chain 'C' and resid 267 through 276 removed outlier: 3.770A pdb=" N ILE C 270 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR C 290 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 326 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'C' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY C 397 " --> pdb=" O VAL C 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA C 406 " --> pdb=" O ASN C 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG C 407 " --> pdb=" O MET C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 444 Processing helix chain 'C' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL C 453 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU C 464 " --> pdb=" O LYS C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 493 removed outlier: 4.235A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C 491 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU C 493 " --> pdb=" O VAL C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 578 through 586 Processing helix chain 'C' and resid 591 through 605 removed outlier: 3.641A pdb=" N LYS C 605 " --> pdb=" O GLN C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 189 removed outlier: 3.524A pdb=" N TYR D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Proline residue: D 175 - end of helix removed outlier: 5.253A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 196 removed outlier: 3.537A pdb=" N TYR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 220 removed outlier: 3.588A pdb=" N ILE D 202 " --> pdb=" O GLU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 242 Processing helix chain 'D' and resid 243 through 253 removed outlier: 3.840A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 258 Processing helix chain 'D' and resid 259 through 264 Processing helix chain 'D' and resid 267 through 276 removed outlier: 3.769A pdb=" N ILE D 270 " --> pdb=" O TYR D 267 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 292 removed outlier: 3.734A pdb=" N MET D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR D 290 " --> pdb=" O GLN D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 326 Processing helix chain 'D' and resid 344 through 361 Processing helix chain 'D' and resid 371 through 424 removed outlier: 3.519A pdb=" N GLY D 397 " --> pdb=" O VAL D 393 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ALA D 406 " --> pdb=" O ASN D 402 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ARG D 407 " --> pdb=" O MET D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 444 Processing helix chain 'D' and resid 449 through 455 removed outlier: 3.525A pdb=" N VAL D 453 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 471 removed outlier: 5.040A pdb=" N GLU D 464 " --> pdb=" O LYS D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 493 removed outlier: 4.236A pdb=" N GLU D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU D 491 " --> pdb=" O LEU D 487 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 550 Processing helix chain 'D' and resid 578 through 586 Processing helix chain 'D' and resid 591 through 605 removed outlier: 3.642A pdb=" N LYS D 605 " --> pdb=" O GLN D 601 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 224 through 225 Processing sheet with id=AA2, first strand: chain 'A' and resid 496 through 500 removed outlier: 7.057A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR A 505 " --> pdb=" O SER A 567 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER A 567 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS A 566 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL A 526 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE A 568 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 524 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 570 " --> pdb=" O GLY A 522 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY A 522 " --> pdb=" O TYR A 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP A 572 " --> pdb=" O LYS A 520 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR B 505 " --> pdb=" O SER B 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER B 567 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS B 566 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL B 526 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ILE B 568 " --> pdb=" O LEU B 524 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU B 524 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR B 570 " --> pdb=" O GLY B 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY B 522 " --> pdb=" O TYR B 570 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASP B 572 " --> pdb=" O LYS B 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AA8, first strand: chain 'C' and resid 496 through 500 removed outlier: 7.057A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR C 505 " --> pdb=" O SER C 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER C 567 " --> pdb=" O TYR C 505 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS C 566 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL C 526 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE C 568 " --> pdb=" O LEU C 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU C 524 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR C 570 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY C 522 " --> pdb=" O TYR C 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP C 572 " --> pdb=" O LYS C 520 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 224 through 225 Processing sheet with id=AB2, first strand: chain 'D' and resid 496 through 500 removed outlier: 7.058A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 505 through 507 removed outlier: 6.494A pdb=" N TYR D 505 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N SER D 567 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LYS D 566 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N VAL D 526 " --> pdb=" O LYS D 566 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 568 " --> pdb=" O LEU D 524 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU D 524 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N TYR D 570 " --> pdb=" O GLY D 522 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLY D 522 " --> pdb=" O TYR D 570 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP D 572 " --> pdb=" O LYS D 520 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2652 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 1.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4358 1.34 - 1.45: 2369 1.45 - 1.57: 8333 1.57 - 1.69: 8 1.69 - 1.81: 128 Bond restraints: 15196 Sorted by residual: bond pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " ideal model delta sigma weight residual 1.582 1.477 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O1A PCG A 701 " pdb=" PA PCG A 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O1A PCG D 701 " pdb=" PA PCG D 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O1A PCG C 701 " pdb=" PA PCG C 701 " ideal model delta sigma weight residual 1.582 1.478 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" C1' PCG B 701 " pdb=" O4' PCG B 701 " ideal model delta sigma weight residual 1.409 1.477 -0.068 2.00e-02 2.50e+03 1.17e+01 ... (remaining 15191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 20211 1.86 - 3.71: 277 3.71 - 5.57: 72 5.57 - 7.43: 24 7.43 - 9.28: 24 Bond angle restraints: 20608 Sorted by residual: angle pdb=" N ARG C 291 " pdb=" CA ARG C 291 " pdb=" C ARG C 291 " ideal model delta sigma weight residual 112.89 119.24 -6.35 1.24e+00 6.50e-01 2.62e+01 angle pdb=" N ARG D 291 " pdb=" CA ARG D 291 " pdb=" C ARG D 291 " ideal model delta sigma weight residual 112.89 119.21 -6.32 1.24e+00 6.50e-01 2.60e+01 angle pdb=" N ARG B 291 " pdb=" CA ARG B 291 " pdb=" C ARG B 291 " ideal model delta sigma weight residual 112.89 119.18 -6.29 1.24e+00 6.50e-01 2.57e+01 angle pdb=" N ARG A 291 " pdb=" CA ARG A 291 " pdb=" C ARG A 291 " ideal model delta sigma weight residual 112.89 119.16 -6.27 1.24e+00 6.50e-01 2.56e+01 angle pdb=" O1A PCG B 701 " pdb=" PA PCG B 701 " pdb=" O3' PCG B 701 " ideal model delta sigma weight residual 100.83 110.11 -9.28 3.00e+00 1.11e-01 9.57e+00 ... (remaining 20603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 8794 28.99 - 57.99: 286 57.99 - 86.98: 8 86.98 - 115.97: 4 115.97 - 144.96: 12 Dihedral angle restraints: 9104 sinusoidal: 3788 harmonic: 5316 Sorted by residual: dihedral pdb=" C3' PCG B 701 " pdb=" O3' PCG B 701 " pdb=" PA PCG B 701 " pdb=" O1A PCG B 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.63 -144.96 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG C 701 " pdb=" O3' PCG C 701 " pdb=" PA PCG C 701 " pdb=" O1A PCG C 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.65 -144.94 1 3.00e+01 1.11e-03 1.94e+01 dihedral pdb=" C3' PCG D 701 " pdb=" O3' PCG D 701 " pdb=" PA PCG D 701 " pdb=" O1A PCG D 701 " ideal model delta sinusoidal sigma weight residual 151.41 -63.68 -144.91 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 9101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2276 0.131 - 0.263: 28 0.263 - 0.394: 4 0.394 - 0.525: 0 0.525 - 0.657: 4 Chirality restraints: 2312 Sorted by residual: chirality pdb=" PA PCG B 701 " pdb=" O2A PCG B 701 " pdb=" O3' PCG B 701 " pdb=" O5' PCG B 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.36 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" PA PCG C 701 " pdb=" O2A PCG C 701 " pdb=" O3' PCG C 701 " pdb=" O5' PCG C 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" PA PCG D 701 " pdb=" O2A PCG D 701 " pdb=" O3' PCG D 701 " pdb=" O5' PCG D 701 " both_signs ideal model delta sigma weight residual True 2.70 -3.35 -0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 2309 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C VAL D 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL D 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL D 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 526 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C VAL C 526 " 0.027 2.00e-02 2.50e+03 pdb=" O VAL C 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 527 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 526 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.29e+00 pdb=" C VAL B 526 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 526 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 527 " -0.009 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2644 2.76 - 3.30: 15656 3.30 - 3.83: 26907 3.83 - 4.37: 32515 4.37 - 4.90: 53421 Nonbonded interactions: 131143 Sorted by model distance: nonbonded pdb=" O PHE B 216 " pdb=" OG1 THR B 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE A 216 " pdb=" OG1 THR A 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE C 216 " pdb=" OG1 THR C 219 " model vdw 2.226 3.040 nonbonded pdb=" O PHE D 216 " pdb=" OG1 THR D 219 " model vdw 2.227 3.040 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.319 3.040 ... (remaining 131138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 156 through 701) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.760 Find NCS groups from input model: 0.320 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:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 15196 Z= 0.230 Angle : 0.696 9.283 20608 Z= 0.370 Chirality : 0.052 0.657 2312 Planarity : 0.003 0.028 2540 Dihedral : 14.963 144.963 5696 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.25 % Allowed : 2.72 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.19), residues: 1792 helix: -0.53 (0.14), residues: 1080 sheet: -1.26 (0.82), residues: 56 loop : -0.92 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 561 TYR 0.014 0.001 TYR C 349 PHE 0.014 0.002 PHE C 389 TRP 0.024 0.002 TRP C 168 HIS 0.003 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00481 (15196) covalent geometry : angle 0.69617 (20608) hydrogen bonds : bond 0.12174 ( 904) hydrogen bonds : angle 6.69145 ( 2652) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 263 time to evaluate : 0.462 Fit side-chains REVERT: A 266 ASN cc_start: 0.7431 (t0) cc_final: 0.7210 (t0) REVERT: A 428 LYS cc_start: 0.7731 (mtpt) cc_final: 0.7404 (mptp) REVERT: A 450 GLU cc_start: 0.6476 (pt0) cc_final: 0.6115 (pp20) REVERT: A 496 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7094 (mt0) REVERT: A 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6228 (mptp) REVERT: B 266 ASN cc_start: 0.7432 (t0) cc_final: 0.7217 (t0) REVERT: B 428 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7399 (mptp) REVERT: B 450 GLU cc_start: 0.6477 (pt0) cc_final: 0.6118 (pp20) REVERT: B 496 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7107 (mt0) REVERT: B 605 LYS cc_start: 0.6441 (ptmt) cc_final: 0.6225 (mptp) REVERT: C 266 ASN cc_start: 0.7427 (t0) cc_final: 0.7206 (t0) REVERT: C 428 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7416 (mptp) REVERT: C 450 GLU cc_start: 0.6478 (pt0) cc_final: 0.6129 (pp20) REVERT: C 496 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7142 (mt0) REVERT: C 605 LYS cc_start: 0.6438 (ptmt) cc_final: 0.6226 (mptp) REVERT: D 266 ASN cc_start: 0.7421 (t0) cc_final: 0.7182 (t0) REVERT: D 428 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7399 (mptp) REVERT: D 450 GLU cc_start: 0.6475 (pt0) cc_final: 0.6117 (pp20) REVERT: D 496 GLN cc_start: 0.7373 (mm-40) cc_final: 0.7089 (mt0) REVERT: D 605 LYS cc_start: 0.6449 (ptmt) cc_final: 0.6219 (mptp) outliers start: 4 outliers final: 4 residues processed: 267 average time/residue: 0.7173 time to fit residues: 206.9071 Evaluate side-chains 174 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 170 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 ARG Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain D residue 291 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 395 ASN A 402 ASN A 468 ASN A 534 GLN B 238 ASN B 302 ASN B 395 ASN B 402 ASN B 468 ASN B 534 GLN C 238 ASN C 395 ASN C 402 ASN C 468 ASN C 534 GLN D 238 ASN D 395 ASN D 402 ASN D 468 ASN D 534 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.156861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.120306 restraints weight = 17662.244| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.71 r_work: 0.3128 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15196 Z= 0.128 Angle : 0.533 7.466 20608 Z= 0.278 Chirality : 0.041 0.152 2312 Planarity : 0.004 0.034 2540 Dihedral : 12.893 154.318 2136 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.68 % Allowed : 9.81 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1792 helix: 0.93 (0.16), residues: 1064 sheet: -0.69 (0.69), residues: 56 loop : -0.47 (0.28), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 347 TYR 0.013 0.001 TYR B 349 PHE 0.013 0.001 PHE D 389 TRP 0.018 0.001 TRP C 168 HIS 0.002 0.001 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00282 (15196) covalent geometry : angle 0.53293 (20608) hydrogen bonds : bond 0.03951 ( 904) hydrogen bonds : angle 4.88159 ( 2652) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.516 Fit side-chains REVERT: A 266 ASN cc_start: 0.7807 (t0) cc_final: 0.7544 (t0) REVERT: A 341 GLU cc_start: 0.7881 (tp30) cc_final: 0.7663 (tp30) REVERT: A 428 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7567 (mptt) REVERT: A 450 GLU cc_start: 0.6611 (pt0) cc_final: 0.6268 (pp20) REVERT: A 496 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7299 (mt0) REVERT: A 605 LYS cc_start: 0.6543 (ptmt) cc_final: 0.6240 (mptp) REVERT: B 266 ASN cc_start: 0.7803 (t0) cc_final: 0.7535 (t0) REVERT: B 428 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7586 (mptt) REVERT: B 450 GLU cc_start: 0.6610 (pt0) cc_final: 0.6295 (pp20) REVERT: B 496 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7311 (mt0) REVERT: B 605 LYS cc_start: 0.6533 (ptmt) cc_final: 0.6226 (mptp) REVERT: C 266 ASN cc_start: 0.7762 (t0) cc_final: 0.7519 (t0) REVERT: C 428 LYS cc_start: 0.7913 (mtpt) cc_final: 0.7610 (mptt) REVERT: C 450 GLU cc_start: 0.6605 (pt0) cc_final: 0.6274 (pp20) REVERT: C 452 GLU cc_start: 0.7973 (tp30) cc_final: 0.7749 (tp30) REVERT: C 496 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7296 (mt0) REVERT: C 605 LYS cc_start: 0.6529 (ptmt) cc_final: 0.6223 (mptp) REVERT: D 266 ASN cc_start: 0.7764 (t0) cc_final: 0.7519 (t0) REVERT: D 428 LYS cc_start: 0.7894 (mtpt) cc_final: 0.7585 (mptt) REVERT: D 450 GLU cc_start: 0.6583 (pt0) cc_final: 0.6255 (pp20) REVERT: D 452 GLU cc_start: 0.7977 (tp30) cc_final: 0.7749 (tp30) REVERT: D 496 GLN cc_start: 0.7588 (mm-40) cc_final: 0.7323 (mt0) REVERT: D 605 LYS cc_start: 0.6521 (ptmt) cc_final: 0.6231 (mptp) outliers start: 11 outliers final: 4 residues processed: 209 average time/residue: 0.6115 time to fit residues: 140.1604 Evaluate side-chains 196 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 399 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 121 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.121269 restraints weight = 17832.581| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.76 r_work: 0.3122 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2024 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= 0.125 Angle : 0.508 7.907 20608 Z= 0.264 Chirality : 0.040 0.144 2312 Planarity : 0.004 0.026 2540 Dihedral : 12.752 151.370 2120 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.80 % Allowed : 12.04 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.21), residues: 1792 helix: 1.21 (0.16), residues: 1068 sheet: -0.08 (0.70), residues: 56 loop : -0.26 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.013 0.001 TYR D 349 PHE 0.011 0.001 PHE C 389 TRP 0.017 0.001 TRP C 168 HIS 0.002 0.001 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00278 (15196) covalent geometry : angle 0.50778 (20608) hydrogen bonds : bond 0.03742 ( 904) hydrogen bonds : angle 4.62540 ( 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 202 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.620 Fit side-chains REVERT: A 266 ASN cc_start: 0.7805 (t0) cc_final: 0.7542 (t0) REVERT: A 428 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7564 (mptt) REVERT: A 450 GLU cc_start: 0.6591 (pt0) cc_final: 0.6280 (pp20) REVERT: A 496 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7256 (mt0) REVERT: A 605 LYS cc_start: 0.6550 (ptmt) cc_final: 0.6252 (mptp) REVERT: B 266 ASN cc_start: 0.7803 (t0) cc_final: 0.7542 (t0) REVERT: B 407 ARG cc_start: 0.7726 (tpt170) cc_final: 0.7434 (tpm-80) REVERT: B 428 LYS cc_start: 0.7838 (mtpt) cc_final: 0.7583 (mptt) REVERT: B 450 GLU cc_start: 0.6595 (pt0) cc_final: 0.6312 (pp20) REVERT: B 496 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7276 (mt0) REVERT: B 605 LYS cc_start: 0.6579 (ptmt) cc_final: 0.6216 (mptp) REVERT: C 266 ASN cc_start: 0.7794 (t0) cc_final: 0.7531 (t0) REVERT: C 407 ARG cc_start: 0.7715 (tpt170) cc_final: 0.7423 (tpm-80) REVERT: C 428 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7587 (mptt) REVERT: C 450 GLU cc_start: 0.6555 (pt0) cc_final: 0.6254 (pp20) REVERT: C 496 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7269 (mt0) REVERT: C 605 LYS cc_start: 0.6553 (ptmt) cc_final: 0.6199 (mptp) REVERT: D 266 ASN cc_start: 0.7793 (t0) cc_final: 0.7534 (t0) REVERT: D 407 ARG cc_start: 0.7711 (tpt170) cc_final: 0.7422 (tpm-80) REVERT: D 428 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7564 (mptt) REVERT: D 450 GLU cc_start: 0.6551 (pt0) cc_final: 0.6266 (pp20) REVERT: D 496 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7266 (mt0) REVERT: D 605 LYS cc_start: 0.6548 (ptmt) cc_final: 0.6202 (mptp) outliers start: 13 outliers final: 4 residues processed: 197 average time/residue: 0.6363 time to fit residues: 136.9996 Evaluate side-chains 181 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 177 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain D residue 399 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 76 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 174 optimal weight: 0.4980 chunk 129 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 chunk 157 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN B 422 HIS C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117744 restraints weight = 17914.011| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.77 r_work: 0.3099 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15196 Z= 0.171 Angle : 0.535 8.137 20608 Z= 0.279 Chirality : 0.041 0.140 2312 Planarity : 0.004 0.028 2540 Dihedral : 12.776 150.216 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.42 % Allowed : 11.85 % Favored : 86.73 % 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: 0.89 (0.20), residues: 1792 helix: 1.20 (0.16), residues: 1068 sheet: 0.18 (0.69), residues: 56 loop : -0.25 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 462 TYR 0.019 0.001 TYR A 349 PHE 0.014 0.002 PHE A 389 TRP 0.020 0.002 TRP C 168 HIS 0.002 0.001 HIS B 422 Details of bonding type rmsd covalent geometry : bond 0.00395 (15196) covalent geometry : angle 0.53471 (20608) hydrogen bonds : bond 0.03913 ( 904) hydrogen bonds : angle 4.69951 ( 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 197 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.522 Fit side-chains REVERT: A 228 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 232 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7146 (mm-30) REVERT: A 266 ASN cc_start: 0.8075 (t0) cc_final: 0.7795 (t0) REVERT: A 428 LYS cc_start: 0.7855 (mtpt) cc_final: 0.7488 (mptt) REVERT: A 450 GLU cc_start: 0.6768 (pt0) cc_final: 0.6358 (pp20) REVERT: A 496 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7397 (mt0) REVERT: A 605 LYS cc_start: 0.6789 (ptmt) cc_final: 0.6386 (mptp) REVERT: B 228 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8263 (mm) REVERT: B 266 ASN cc_start: 0.8090 (t0) cc_final: 0.7811 (t0) REVERT: B 428 LYS cc_start: 0.7878 (mtpt) cc_final: 0.7531 (mptt) REVERT: B 450 GLU cc_start: 0.6750 (pt0) cc_final: 0.6315 (pp20) REVERT: B 496 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7380 (mt0) REVERT: B 605 LYS cc_start: 0.6796 (ptmt) cc_final: 0.6388 (mptp) REVERT: C 232 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7079 (mm-30) REVERT: C 266 ASN cc_start: 0.8074 (t0) cc_final: 0.7799 (t0) REVERT: C 428 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7512 (mptt) REVERT: C 450 GLU cc_start: 0.6755 (pt0) cc_final: 0.6318 (pp20) REVERT: C 496 GLN cc_start: 0.7664 (mm-40) cc_final: 0.7350 (mt0) REVERT: C 605 LYS cc_start: 0.6787 (ptmt) cc_final: 0.6380 (mptp) REVERT: D 228 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8258 (mm) REVERT: D 266 ASN cc_start: 0.8073 (t0) cc_final: 0.7797 (t0) REVERT: D 428 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7496 (mptt) REVERT: D 450 GLU cc_start: 0.6769 (pt0) cc_final: 0.6336 (pp20) REVERT: D 496 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7382 (mt0) REVERT: D 605 LYS cc_start: 0.6793 (ptmt) cc_final: 0.6369 (mptp) outliers start: 23 outliers final: 11 residues processed: 186 average time/residue: 0.6792 time to fit residues: 136.9158 Evaluate side-chains 174 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 141 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 144 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.119328 restraints weight = 17873.051| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.70 r_work: 0.3120 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15196 Z= 0.148 Angle : 0.515 7.732 20608 Z= 0.268 Chirality : 0.040 0.142 2312 Planarity : 0.004 0.027 2540 Dihedral : 12.704 149.470 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.48 % Allowed : 12.35 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1792 helix: 1.23 (0.16), residues: 1068 sheet: 0.20 (0.66), residues: 56 loop : -0.14 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 462 TYR 0.016 0.001 TYR C 349 PHE 0.012 0.001 PHE D 535 TRP 0.020 0.002 TRP C 168 HIS 0.001 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00339 (15196) covalent geometry : angle 0.51502 (20608) hydrogen bonds : bond 0.03786 ( 904) hydrogen bonds : angle 4.61832 ( 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 200 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.612 Fit side-chains REVERT: A 228 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8239 (mm) REVERT: A 232 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 266 ASN cc_start: 0.8013 (t0) cc_final: 0.7753 (t0) REVERT: A 428 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7524 (mptt) REVERT: A 450 GLU cc_start: 0.6749 (pt0) cc_final: 0.6347 (pp20) REVERT: A 496 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7337 (mt0) REVERT: A 605 LYS cc_start: 0.6840 (ptmt) cc_final: 0.6402 (mptp) REVERT: B 228 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 232 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7038 (mm-30) REVERT: B 266 ASN cc_start: 0.8010 (t0) cc_final: 0.7760 (t0) REVERT: B 428 LYS cc_start: 0.7884 (mtpt) cc_final: 0.7545 (mptt) REVERT: B 450 GLU cc_start: 0.6743 (pt0) cc_final: 0.6327 (pp20) REVERT: B 496 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7354 (mt0) REVERT: B 605 LYS cc_start: 0.6840 (ptmt) cc_final: 0.6406 (mptp) REVERT: C 228 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8218 (mm) REVERT: C 232 GLU cc_start: 0.7270 (mm-30) cc_final: 0.7025 (mm-30) REVERT: C 266 ASN cc_start: 0.7993 (t0) cc_final: 0.7732 (t0) REVERT: C 428 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7575 (mptt) REVERT: C 450 GLU cc_start: 0.6730 (pt0) cc_final: 0.6312 (pp20) REVERT: C 496 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7348 (mt0) REVERT: C 605 LYS cc_start: 0.6802 (ptmt) cc_final: 0.6382 (mptp) REVERT: D 228 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8252 (mm) REVERT: D 232 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7151 (mm-30) REVERT: D 266 ASN cc_start: 0.8005 (t0) cc_final: 0.7742 (t0) REVERT: D 428 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7518 (mptt) REVERT: D 450 GLU cc_start: 0.6701 (pt0) cc_final: 0.6303 (pp20) REVERT: D 496 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7359 (mt0) REVERT: D 605 LYS cc_start: 0.6833 (ptmt) cc_final: 0.6398 (mptp) outliers start: 24 outliers final: 12 residues processed: 184 average time/residue: 0.6508 time to fit residues: 130.4992 Evaluate side-chains 182 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 135 optimal weight: 7.9990 chunk 27 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 155 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117548 restraints weight = 17785.048| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.77 r_work: 0.3082 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15196 Z= 0.182 Angle : 0.549 9.292 20608 Z= 0.283 Chirality : 0.041 0.140 2312 Planarity : 0.004 0.028 2540 Dihedral : 12.724 147.387 2120 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.30 % Allowed : 13.64 % Favored : 85.06 % 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: 0.93 (0.20), residues: 1792 helix: 1.18 (0.16), residues: 1068 sheet: 0.12 (0.63), residues: 56 loop : -0.12 (0.26), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 347 TYR 0.018 0.002 TYR B 349 PHE 0.015 0.002 PHE A 389 TRP 0.021 0.002 TRP D 168 HIS 0.002 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00421 (15196) covalent geometry : angle 0.54872 (20608) hydrogen bonds : bond 0.03958 ( 904) hydrogen bonds : angle 4.71230 ( 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 188 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.579 Fit side-chains REVERT: A 266 ASN cc_start: 0.7794 (t0) cc_final: 0.7582 (t0) REVERT: A 428 LYS cc_start: 0.7803 (mtpt) cc_final: 0.7507 (mptt) REVERT: A 450 GLU cc_start: 0.6645 (pt0) cc_final: 0.6303 (pp20) REVERT: A 496 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7316 (mt0) REVERT: A 605 LYS cc_start: 0.6910 (ptmt) cc_final: 0.6528 (mptp) REVERT: B 266 ASN cc_start: 0.7804 (t0) cc_final: 0.7590 (t0) REVERT: B 428 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7517 (mptt) REVERT: B 450 GLU cc_start: 0.6690 (pt0) cc_final: 0.6373 (pp20) REVERT: B 496 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7298 (mt0) REVERT: B 605 LYS cc_start: 0.6903 (ptmt) cc_final: 0.6545 (mptp) REVERT: C 228 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8147 (mm) REVERT: C 266 ASN cc_start: 0.7810 (t0) cc_final: 0.7596 (t0) REVERT: C 428 LYS cc_start: 0.7824 (mtpt) cc_final: 0.7511 (mptt) REVERT: C 450 GLU cc_start: 0.6747 (pt0) cc_final: 0.6376 (pp20) REVERT: C 496 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7302 (mt0) REVERT: C 605 LYS cc_start: 0.6908 (ptmt) cc_final: 0.6535 (mptp) REVERT: D 232 GLU cc_start: 0.7217 (mm-30) cc_final: 0.7016 (mm-30) REVERT: D 266 ASN cc_start: 0.7803 (t0) cc_final: 0.7593 (t0) REVERT: D 428 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7495 (mptt) REVERT: D 450 GLU cc_start: 0.6728 (pt0) cc_final: 0.6356 (pp20) REVERT: D 496 GLN cc_start: 0.7632 (mm-40) cc_final: 0.7319 (mt0) REVERT: D 605 LYS cc_start: 0.6902 (ptmt) cc_final: 0.6527 (mptp) outliers start: 21 outliers final: 16 residues processed: 176 average time/residue: 0.6456 time to fit residues: 124.1409 Evaluate side-chains 174 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 137 optimal weight: 0.9990 chunk 176 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 147 optimal weight: 0.6980 chunk 178 optimal weight: 0.0040 chunk 97 optimal weight: 7.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN B 395 ASN B 419 GLN C 395 ASN C 419 GLN D 395 ASN D 419 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124408 restraints weight = 17779.550| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.74 r_work: 0.3188 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15196 Z= 0.109 Angle : 0.498 8.735 20608 Z= 0.253 Chirality : 0.039 0.146 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.599 149.114 2120 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.05 % Allowed : 14.32 % Favored : 84.63 % 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: 1.34 (0.20), residues: 1792 helix: 1.51 (0.16), residues: 1064 sheet: 0.69 (0.68), residues: 48 loop : 0.02 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 218 TYR 0.012 0.001 TYR C 199 PHE 0.010 0.001 PHE C 535 TRP 0.019 0.001 TRP D 168 HIS 0.001 0.000 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00240 (15196) covalent geometry : angle 0.49761 (20608) hydrogen bonds : bond 0.03452 ( 904) hydrogen bonds : angle 4.43173 ( 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 182 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.662 Fit side-chains REVERT: A 266 ASN cc_start: 0.7896 (t0) cc_final: 0.7618 (t0) REVERT: A 428 LYS cc_start: 0.7750 (mtpt) cc_final: 0.7484 (mptt) REVERT: A 450 GLU cc_start: 0.6642 (pt0) cc_final: 0.6270 (pp20) REVERT: A 496 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7356 (mt0) REVERT: A 540 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: A 605 LYS cc_start: 0.6762 (ptmt) cc_final: 0.6408 (mptp) REVERT: B 266 ASN cc_start: 0.7881 (t0) cc_final: 0.7623 (t0) REVERT: B 428 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7503 (mptt) REVERT: B 450 GLU cc_start: 0.6609 (pt0) cc_final: 0.6265 (pp20) REVERT: B 496 GLN cc_start: 0.7676 (mm-40) cc_final: 0.7356 (mt0) REVERT: B 540 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6801 (m-30) REVERT: B 605 LYS cc_start: 0.6759 (ptmt) cc_final: 0.6420 (mptp) REVERT: C 266 ASN cc_start: 0.7883 (t0) cc_final: 0.7608 (t0) REVERT: C 428 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7518 (mptt) REVERT: C 450 GLU cc_start: 0.6654 (pt0) cc_final: 0.6268 (pp20) REVERT: C 496 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7330 (mt0) REVERT: C 540 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.7116 (m-30) REVERT: C 605 LYS cc_start: 0.6751 (ptmt) cc_final: 0.6404 (mptp) REVERT: D 232 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6958 (mm-30) REVERT: D 266 ASN cc_start: 0.7872 (t0) cc_final: 0.7598 (t0) REVERT: D 389 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: D 428 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7483 (mptt) REVERT: D 450 GLU cc_start: 0.6655 (pt0) cc_final: 0.6264 (pp20) REVERT: D 496 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7320 (mt0) REVERT: D 540 ASP cc_start: 0.7285 (OUTLIER) cc_final: 0.6819 (m-30) REVERT: D 605 LYS cc_start: 0.6773 (ptmt) cc_final: 0.6424 (mptp) outliers start: 17 outliers final: 12 residues processed: 170 average time/residue: 0.6471 time to fit residues: 120.1031 Evaluate side-chains 165 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 166 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 157 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 171 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 402 ASN A 419 GLN A 422 HIS B 395 ASN B 419 GLN B 422 HIS C 395 ASN C 419 GLN C 422 HIS D 395 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120268 restraints weight = 17874.952| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.73 r_work: 0.3112 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2625 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= 0.140 Angle : 0.524 8.390 20608 Z= 0.267 Chirality : 0.040 0.141 2312 Planarity : 0.004 0.035 2540 Dihedral : 12.624 148.266 2120 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.36 % Allowed : 15.00 % Favored : 83.64 % 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: 1.33 (0.20), residues: 1792 helix: 1.51 (0.16), residues: 1064 sheet: 0.53 (0.67), residues: 48 loop : 0.01 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.014 0.001 TYR A 349 PHE 0.013 0.001 PHE C 535 TRP 0.019 0.001 TRP B 168 HIS 0.001 0.001 HIS D 422 Details of bonding type rmsd covalent geometry : bond 0.00321 (15196) covalent geometry : angle 0.52386 (20608) hydrogen bonds : bond 0.03663 ( 904) hydrogen bonds : angle 4.50850 ( 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 168 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.589 Fit side-chains REVERT: A 266 ASN cc_start: 0.7777 (t0) cc_final: 0.7519 (t0) REVERT: A 389 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: A 428 LYS cc_start: 0.7700 (mtpt) cc_final: 0.7477 (mptt) REVERT: A 450 GLU cc_start: 0.6630 (pt0) cc_final: 0.6293 (pp20) REVERT: A 496 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7293 (mt0) REVERT: A 605 LYS cc_start: 0.6739 (ptmt) cc_final: 0.6372 (mptp) REVERT: B 266 ASN cc_start: 0.7778 (t0) cc_final: 0.7519 (t0) REVERT: B 389 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: B 428 LYS cc_start: 0.7710 (mtpt) cc_final: 0.7493 (mptt) REVERT: B 450 GLU cc_start: 0.6649 (pt0) cc_final: 0.6314 (pp20) REVERT: B 496 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7281 (mt0) REVERT: B 605 LYS cc_start: 0.6773 (ptmt) cc_final: 0.6410 (mptp) REVERT: C 266 ASN cc_start: 0.7773 (t0) cc_final: 0.7520 (t0) REVERT: C 389 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: C 428 LYS cc_start: 0.7705 (mtpt) cc_final: 0.7487 (mptt) REVERT: C 450 GLU cc_start: 0.6638 (pt0) cc_final: 0.6289 (pp20) REVERT: C 496 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7274 (mt0) REVERT: C 605 LYS cc_start: 0.6748 (ptmt) cc_final: 0.6382 (mptp) REVERT: D 232 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7031 (mm-30) REVERT: D 266 ASN cc_start: 0.7735 (t0) cc_final: 0.7490 (t0) REVERT: D 389 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8119 (m-80) REVERT: D 428 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7494 (mptt) REVERT: D 450 GLU cc_start: 0.6611 (pt0) cc_final: 0.6282 (pp20) REVERT: D 496 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7285 (mt0) REVERT: D 605 LYS cc_start: 0.6773 (ptmt) cc_final: 0.6406 (mptp) outliers start: 22 outliers final: 16 residues processed: 156 average time/residue: 0.6232 time to fit residues: 106.8020 Evaluate side-chains 163 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 594 MET Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 540 ASP Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 594 MET Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 150 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 0.0070 chunk 89 optimal weight: 6.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 ASN A 419 GLN A 422 HIS B 395 ASN B 402 ASN B 419 GLN B 422 HIS C 395 ASN C 402 ASN C 419 GLN C 422 HIS D 395 ASN D 402 ASN D 419 GLN D 422 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.157295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.124413 restraints weight = 17965.620| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.70 r_work: 0.3187 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15196 Z= 0.108 Angle : 0.497 8.044 20608 Z= 0.252 Chirality : 0.039 0.145 2312 Planarity : 0.003 0.029 2540 Dihedral : 12.566 149.556 2120 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.11 % Allowed : 15.06 % Favored : 83.83 % 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: 1.50 (0.20), residues: 1792 helix: 1.66 (0.16), residues: 1064 sheet: 0.59 (0.68), residues: 48 loop : 0.07 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 413 TYR 0.011 0.001 TYR B 199 PHE 0.012 0.001 PHE C 535 TRP 0.019 0.001 TRP B 168 HIS 0.001 0.001 HIS C 312 Details of bonding type rmsd covalent geometry : bond 0.00240 (15196) covalent geometry : angle 0.49660 (20608) hydrogen bonds : bond 0.03410 ( 904) hydrogen bonds : angle 4.37460 ( 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 174 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.560 Fit side-chains REVERT: A 266 ASN cc_start: 0.7902 (t0) cc_final: 0.7618 (t0) REVERT: A 450 GLU cc_start: 0.6654 (pt0) cc_final: 0.6277 (pp20) REVERT: A 496 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7343 (mt0) REVERT: A 605 LYS cc_start: 0.6717 (ptmt) cc_final: 0.6329 (mptp) REVERT: B 266 ASN cc_start: 0.7892 (t0) cc_final: 0.7616 (t0) REVERT: B 450 GLU cc_start: 0.6651 (pt0) cc_final: 0.6269 (pp20) REVERT: B 496 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7353 (mt0) REVERT: B 605 LYS cc_start: 0.6709 (ptmt) cc_final: 0.6347 (mptp) REVERT: C 266 ASN cc_start: 0.7887 (t0) cc_final: 0.7612 (t0) REVERT: C 431 GLU cc_start: 0.8154 (tt0) cc_final: 0.7726 (mt-10) REVERT: C 450 GLU cc_start: 0.6664 (pt0) cc_final: 0.6278 (pp20) REVERT: C 496 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7302 (mt0) REVERT: C 540 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: C 605 LYS cc_start: 0.6733 (ptmt) cc_final: 0.6345 (mptp) REVERT: D 232 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6981 (mm-30) REVERT: D 266 ASN cc_start: 0.7861 (t0) cc_final: 0.7581 (t0) REVERT: D 428 LYS cc_start: 0.7660 (mtpt) cc_final: 0.7451 (mptt) REVERT: D 450 GLU cc_start: 0.6622 (pt0) cc_final: 0.6247 (pp20) REVERT: D 496 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7327 (mt0) REVERT: D 605 LYS cc_start: 0.6739 (ptmt) cc_final: 0.6350 (mptp) outliers start: 18 outliers final: 9 residues processed: 162 average time/residue: 0.5996 time to fit residues: 106.7052 Evaluate side-chains 156 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 245 GLN A 395 ASN A 419 GLN A 422 HIS A 444 ASN B 245 GLN B 395 ASN B 419 GLN B 444 ASN C 245 GLN C 395 ASN C 419 GLN C 422 HIS C 444 ASN D 226 GLN D 245 GLN D 395 ASN D 419 GLN D 444 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118322 restraints weight = 17850.627| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.69 r_work: 0.3095 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15196 Z= 0.186 Angle : 0.557 8.311 20608 Z= 0.286 Chirality : 0.041 0.141 2312 Planarity : 0.004 0.031 2540 Dihedral : 12.678 147.385 2120 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.23 % Allowed : 16.05 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.20), residues: 1792 helix: 1.25 (0.15), residues: 1092 sheet: 0.42 (0.66), residues: 48 loop : 0.02 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.019 0.002 TYR A 349 PHE 0.016 0.002 PHE D 389 TRP 0.019 0.002 TRP D 168 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00433 (15196) covalent geometry : angle 0.55676 (20608) hydrogen bonds : bond 0.03919 ( 904) hydrogen bonds : angle 4.63297 ( 2652) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.401 Fit side-chains REVERT: A 226 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7752 (tp40) REVERT: A 266 ASN cc_start: 0.8014 (t0) cc_final: 0.7774 (t0) REVERT: A 389 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.8363 (m-80) REVERT: A 395 ASN cc_start: 0.7017 (m-40) cc_final: 0.6388 (t0) REVERT: A 450 GLU cc_start: 0.6758 (pt0) cc_final: 0.6364 (pp20) REVERT: A 475 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7574 (ptpt) REVERT: A 496 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7420 (mt0) REVERT: A 605 LYS cc_start: 0.6941 (ptmt) cc_final: 0.6499 (mptp) REVERT: B 266 ASN cc_start: 0.8034 (t0) cc_final: 0.7787 (t0) REVERT: B 389 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8360 (m-80) REVERT: B 395 ASN cc_start: 0.7016 (m-40) cc_final: 0.6399 (t0) REVERT: B 450 GLU cc_start: 0.6740 (pt0) cc_final: 0.6360 (pp20) REVERT: B 475 LYS cc_start: 0.8097 (mmtt) cc_final: 0.7523 (ptpt) REVERT: B 496 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7418 (mt0) REVERT: B 605 LYS cc_start: 0.7031 (ptmt) cc_final: 0.6577 (mptp) REVERT: C 266 ASN cc_start: 0.8033 (t0) cc_final: 0.7795 (t0) REVERT: C 389 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: C 395 ASN cc_start: 0.7030 (m-40) cc_final: 0.6412 (t0) REVERT: C 450 GLU cc_start: 0.6745 (pt0) cc_final: 0.6337 (pp20) REVERT: C 475 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7608 (ptpt) REVERT: C 496 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7413 (mt0) REVERT: C 540 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7187 (m-30) REVERT: C 605 LYS cc_start: 0.7016 (ptmt) cc_final: 0.6536 (mptp) REVERT: D 232 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7084 (mm-30) REVERT: D 266 ASN cc_start: 0.7992 (t0) cc_final: 0.7755 (t0) REVERT: D 389 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8366 (m-80) REVERT: D 395 ASN cc_start: 0.7041 (m-40) cc_final: 0.6393 (t0) REVERT: D 428 LYS cc_start: 0.7730 (mtpt) cc_final: 0.7501 (mptt) REVERT: D 450 GLU cc_start: 0.6723 (pt0) cc_final: 0.6315 (pp20) REVERT: D 475 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7581 (ptpt) REVERT: D 496 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7389 (mt0) REVERT: D 605 LYS cc_start: 0.7017 (ptmt) cc_final: 0.6545 (mptp) outliers start: 20 outliers final: 10 residues processed: 169 average time/residue: 0.6309 time to fit residues: 116.7674 Evaluate side-chains 167 residues out of total 1624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLN Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 MET Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain C residue 389 PHE Chi-restraints excluded: chain C residue 399 MET Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain C residue 593 THR Chi-restraints excluded: chain D residue 226 GLN Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 593 THR Chi-restraints excluded: chain D residue 594 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 7 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 125 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN C 419 GLN D 419 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120404 restraints weight = 17891.226| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.73 r_work: 0.3135 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15196 Z= 0.126 Angle : 0.520 8.199 20608 Z= 0.266 Chirality : 0.040 0.142 2312 Planarity : 0.004 0.029 2540 Dihedral : 12.614 148.325 2120 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.86 % Allowed : 16.42 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.20), residues: 1792 helix: 1.39 (0.16), residues: 1088 sheet: 0.49 (0.67), residues: 48 loop : 0.01 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 413 TYR 0.013 0.001 TYR A 349 PHE 0.012 0.001 PHE C 535 TRP 0.020 0.001 TRP D 168 HIS 0.001 0.000 HIS B 312 Details of bonding type rmsd covalent geometry : bond 0.00284 (15196) covalent geometry : angle 0.52021 (20608) hydrogen bonds : bond 0.03652 ( 904) hydrogen bonds : angle 4.50878 ( 2652) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4503.53 seconds wall clock time: 77 minutes 36.70 seconds (4656.70 seconds total)