Starting phenix.real_space_refine on Thu Mar 5 08:47:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o20_0607/03_2026/6o20_0607.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o20_0607/03_2026/6o20_0607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o20_0607/03_2026/6o20_0607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o20_0607/03_2026/6o20_0607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o20_0607/03_2026/6o20_0607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o20_0607/03_2026/6o20_0607.map" } resolution = 3.3 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= 0.002 sd= 0.034 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 149 5.16 5 C 13497 2.51 5 N 3549 2.21 5 O 3751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 129 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: 20950 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5009 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 601} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 115 Classifications: {'peptide': 13} Link IDs: {'TRANS': 12} Chain: "F" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1125 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 145} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4899 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.14, per 1000 atoms: 0.25 Number of scatterers: 20950 At special positions: 0 Unit cell: (128.139, 128.139, 126.021, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 149 16.00 O 3751 8.00 N 3549 7.00 C 13497 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: 1.70 Conformation dependent library (CDL) restraints added in 1.1 seconds 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4952 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 4 sheets defined 61.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.696A pdb=" N ARG A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.610A pdb=" N TYR A 89 " --> pdb=" O VAL A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 106 removed outlier: 3.578A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.731A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.688A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 172 Processing helix chain 'A' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU A 184 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.773A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 261 through 264 removed outlier: 4.028A pdb=" N LYS A 264 " --> pdb=" O GLN A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 264' Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.821A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 403 removed outlier: 3.717A pdb=" N GLY A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 4.532A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 404 through 409' Processing helix chain 'A' and resid 425 through 443 removed outlier: 3.981A pdb=" N VAL A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 456 " --> pdb=" O VAL A 452 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 3.566A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 512 removed outlier: 4.192A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.639A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 561 " --> pdb=" O ILE A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 581 removed outlier: 3.607A pdb=" N ILE A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 removed outlier: 3.710A pdb=" N ALA A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 653 removed outlier: 4.342A pdb=" N ARG A 646 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N TYR A 647 " --> pdb=" O ARG A 643 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE A 651 " --> pdb=" O TYR A 647 " (cutoff:3.500A) Processing helix chain 'E' and resid 699 through 710 removed outlier: 3.737A pdb=" N ILE E 704 " --> pdb=" O ARG E 700 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 705 " --> pdb=" O GLY E 701 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR E 709 " --> pdb=" O LEU E 705 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU E 710 " --> pdb=" O ARG E 706 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.739A pdb=" N ALA F 10 " --> pdb=" O GLU F 6 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.784A pdb=" N VAL F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 39 " --> pdb=" O VAL F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 53 Processing helix chain 'F' and resid 64 through 75 removed outlier: 3.669A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET F 72 " --> pdb=" O PHE F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 removed outlier: 3.913A pdb=" N ARG F 90 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL F 91 " --> pdb=" O GLU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 113 removed outlier: 3.640A pdb=" N MET F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN F 111 " --> pdb=" O HIS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 137 through 144 Processing helix chain 'B' and resid 28 through 47 removed outlier: 3.697A pdb=" N ARG B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.611A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.578A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.730A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.688A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU B 184 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.774A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 261 through 264 removed outlier: 4.029A pdb=" N LYS B 264 " --> pdb=" O GLN B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 264' Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE B 319 " --> pdb=" O GLU B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.821A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 403 removed outlier: 3.718A pdb=" N GLY B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 4.533A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 409' Processing helix chain 'B' and resid 425 through 443 removed outlier: 3.980A pdb=" N VAL B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE B 456 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET B 466 " --> pdb=" O CYS B 463 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 3.565A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET B 481 " --> pdb=" O PRO B 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN B 483 " --> pdb=" O THR B 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 512 removed outlier: 4.192A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.638A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 581 removed outlier: 3.608A pdb=" N ILE B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 608 removed outlier: 3.709A pdb=" N ALA B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.697A pdb=" N ARG C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.611A pdb=" N TYR C 89 " --> pdb=" O VAL C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 106 removed outlier: 3.578A pdb=" N LEU C 105 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.730A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.687A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 172 Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU C 203 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.773A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 261 through 264 removed outlier: 4.028A pdb=" N LYS C 264 " --> pdb=" O GLN C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 261 through 264' Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 349 removed outlier: 3.821A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 349 " --> pdb=" O THR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 403 removed outlier: 3.718A pdb=" N GLY C 388 " --> pdb=" O ILE C 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 398 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.532A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 425 through 443 removed outlier: 3.980A pdb=" N VAL C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE C 456 " --> pdb=" O VAL C 452 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET C 466 " --> pdb=" O CYS C 463 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 3.566A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN C 483 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 512 removed outlier: 4.192A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.639A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 561 " --> pdb=" O ILE C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 581 removed outlier: 3.607A pdb=" N ILE C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 608 removed outlier: 3.710A pdb=" N ALA C 595 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 47 removed outlier: 3.696A pdb=" N ARG D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 removed outlier: 3.532A pdb=" N ASN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.610A pdb=" N TYR D 89 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.602A pdb=" N ALA D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 106 removed outlier: 3.577A pdb=" N LEU D 105 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.730A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.688A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 Processing helix chain 'D' and resid 175 through 184 removed outlier: 3.707A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 203 removed outlier: 3.507A pdb=" N LEU D 203 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.662A pdb=" N ALA D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.813A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.773A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 261 through 264 removed outlier: 4.029A pdb=" N LYS D 264 " --> pdb=" O GLN D 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 261 through 264' Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.881A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 323 removed outlier: 3.537A pdb=" N PHE D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 349 removed outlier: 3.822A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE D 337 " --> pdb=" O ALA D 333 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR D 349 " --> pdb=" O THR D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 403 removed outlier: 3.717A pdb=" N GLY D 388 " --> pdb=" O ILE D 384 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 398 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 4.532A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 404 through 409' Processing helix chain 'D' and resid 425 through 443 removed outlier: 3.981A pdb=" N VAL D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.689A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE D 456 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 removed outlier: 4.073A pdb=" N MET D 466 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 3.565A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET D 481 " --> pdb=" O PRO D 477 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN D 483 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 512 removed outlier: 4.191A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.639A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.718A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 561 " --> pdb=" O ILE D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 581 removed outlier: 3.607A pdb=" N ILE D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 608 removed outlier: 3.710A pdb=" N ALA D 595 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 273 through 278 Processing sheet with id=AA2, first strand: chain 'B' and resid 273 through 278 Processing sheet with id=AA3, first strand: chain 'C' and resid 273 through 278 Processing sheet with id=AA4, first strand: chain 'D' and resid 273 through 278 871 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.79 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5506 1.33 - 1.45: 4024 1.45 - 1.57: 11643 1.57 - 1.69: 0 1.69 - 1.81: 246 Bond restraints: 21419 Sorted by residual: bond pdb=" CA LYS F 30 " pdb=" C LYS F 30 " ideal model delta sigma weight residual 1.522 1.456 0.065 1.32e-02 5.74e+03 2.45e+01 bond pdb=" C VAL D 452 " pdb=" N PRO D 453 " ideal model delta sigma weight residual 1.337 1.362 -0.025 1.06e-02 8.90e+03 5.63e+00 bond pdb=" C VAL B 452 " pdb=" N PRO B 453 " ideal model delta sigma weight residual 1.337 1.361 -0.025 1.06e-02 8.90e+03 5.41e+00 bond pdb=" C VAL C 452 " pdb=" N PRO C 453 " ideal model delta sigma weight residual 1.337 1.361 -0.025 1.06e-02 8.90e+03 5.36e+00 bond pdb=" C VAL A 452 " pdb=" N PRO A 453 " ideal model delta sigma weight residual 1.337 1.361 -0.024 1.06e-02 8.90e+03 5.30e+00 ... (remaining 21414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 28523 3.34 - 6.69: 464 6.69 - 10.03: 73 10.03 - 13.37: 12 13.37 - 16.71: 1 Bond angle restraints: 29073 Sorted by residual: angle pdb=" N MET F 76 " pdb=" CA MET F 76 " pdb=" C MET F 76 " ideal model delta sigma weight residual 111.24 94.53 16.71 1.38e+00 5.25e-01 1.47e+02 angle pdb=" N ILE A 420 " pdb=" CA ILE A 420 " pdb=" C ILE A 420 " ideal model delta sigma weight residual 111.56 106.01 5.55 8.60e-01 1.35e+00 4.16e+01 angle pdb=" N ILE D 420 " pdb=" CA ILE D 420 " pdb=" C ILE D 420 " ideal model delta sigma weight residual 111.56 106.02 5.54 8.60e-01 1.35e+00 4.15e+01 angle pdb=" N ILE C 420 " pdb=" CA ILE C 420 " pdb=" C ILE C 420 " ideal model delta sigma weight residual 111.56 106.03 5.53 8.60e-01 1.35e+00 4.13e+01 angle pdb=" N ILE B 420 " pdb=" CA ILE B 420 " pdb=" C ILE B 420 " ideal model delta sigma weight residual 111.56 106.04 5.52 8.60e-01 1.35e+00 4.12e+01 ... (remaining 29068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11237 17.97 - 35.94: 1225 35.94 - 53.92: 237 53.92 - 71.89: 31 71.89 - 89.86: 28 Dihedral angle restraints: 12758 sinusoidal: 5097 harmonic: 7661 Sorted by residual: dihedral pdb=" CA ASN F 60 " pdb=" C ASN F 60 " pdb=" N GLY F 61 " pdb=" CA GLY F 61 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA TYR B 623 " pdb=" C TYR B 623 " pdb=" N GLY B 624 " pdb=" CA GLY B 624 " ideal model delta harmonic sigma weight residual 180.00 -154.78 -25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA TYR A 623 " pdb=" C TYR A 623 " pdb=" N GLY A 624 " pdb=" CA GLY A 624 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 12755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3054 0.097 - 0.194: 229 0.194 - 0.291: 21 0.291 - 0.388: 1 0.388 - 0.485: 2 Chirality restraints: 3307 Sorted by residual: chirality pdb=" CB VAL F 136 " pdb=" CA VAL F 136 " pdb=" CG1 VAL F 136 " pdb=" CG2 VAL F 136 " both_signs ideal model delta sigma weight residual False -2.63 -2.14 -0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA SER F 101 " pdb=" N SER F 101 " pdb=" C SER F 101 " pdb=" CB SER F 101 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" CA MET F 76 " pdb=" N MET F 76 " pdb=" C MET F 76 " pdb=" CB MET F 76 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 3304 not shown) Planarity restraints: 3701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR F 99 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C TYR F 99 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR F 99 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE F 100 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 526 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO D 527 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO D 527 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 527 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 526 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 527 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.037 5.00e-02 4.00e+02 ... (remaining 3698 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 186 2.59 - 3.17: 16764 3.17 - 3.75: 32201 3.75 - 4.32: 45455 4.32 - 4.90: 73626 Nonbonded interactions: 168232 Sorted by model distance: nonbonded pdb=" NH1 ARG C 632 " pdb=" OD1 ASP D 34 " model vdw 2.014 3.120 nonbonded pdb=" OE1 GLU C 403 " pdb=" OH TYR C 415 " model vdw 2.021 3.040 nonbonded pdb=" OE1 GLU D 403 " pdb=" OH TYR D 415 " model vdw 2.022 3.040 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 415 " model vdw 2.022 3.040 nonbonded pdb=" OE1 GLU B 403 " pdb=" OH TYR B 415 " model vdw 2.022 3.040 ... (remaining 168227 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 27 through 638) 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.460 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 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 : 0.008 0.065 21419 Z= 0.362 Angle : 1.090 16.713 29073 Z= 0.603 Chirality : 0.058 0.485 3307 Planarity : 0.007 0.065 3701 Dihedral : 15.646 89.860 7806 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 0.40 % Allowed : 10.93 % Favored : 88.67 % Cbeta Deviations : 0.04 % 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: -5.94 (0.11), residues: 2612 helix: -4.42 (0.06), residues: 1527 sheet: -3.92 (0.42), residues: 76 loop : -2.79 (0.16), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 700 TYR 0.014 0.002 TYR D 621 PHE 0.015 0.002 PHE B 115 TRP 0.010 0.002 TRP B 613 HIS 0.005 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00818 (21419) covalent geometry : angle 1.08957 (29073) hydrogen bonds : bond 0.31875 ( 871) hydrogen bonds : angle 10.48862 ( 2457) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 787 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8255 (mmm-85) REVERT: A 99 MET cc_start: 0.7439 (mtp) cc_final: 0.7196 (mtt) REVERT: A 126 MET cc_start: 0.8287 (mmm) cc_final: 0.7917 (mtm) REVERT: A 162 TYR cc_start: 0.8482 (m-10) cc_final: 0.8125 (m-10) REVERT: A 164 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 188 ASP cc_start: 0.7583 (p0) cc_final: 0.7318 (p0) REVERT: A 314 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8217 (tttp) REVERT: A 323 LYS cc_start: 0.8433 (tptp) cc_final: 0.7972 (tptt) REVERT: A 407 ILE cc_start: 0.8446 (mm) cc_final: 0.8162 (mt) REVERT: A 418 GLN cc_start: 0.7011 (tp-100) cc_final: 0.6294 (tp-100) REVERT: A 442 MET cc_start: 0.8450 (mmm) cc_final: 0.8210 (mmt) REVERT: A 485 MET cc_start: 0.7724 (mmt) cc_final: 0.7087 (mmt) REVERT: A 522 GLU cc_start: 0.8538 (mp0) cc_final: 0.8054 (mp0) REVERT: A 553 PHE cc_start: 0.6984 (t80) cc_final: 0.6261 (p90) REVERT: A 637 HIS cc_start: 0.7654 (p-80) cc_final: 0.7267 (p90) REVERT: F 71 MET cc_start: 0.7441 (tpp) cc_final: 0.7188 (tpp) REVERT: F 75 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7278 (mmtp) REVERT: F 86 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6926 (ttp-170) REVERT: F 118 ASP cc_start: 0.8199 (t0) cc_final: 0.7960 (t0) REVERT: F 123 GLU cc_start: 0.7794 (tp30) cc_final: 0.7589 (tp30) REVERT: F 135 GLN cc_start: 0.8855 (mp10) cc_final: 0.8528 (mp10) REVERT: F 139 GLU cc_start: 0.7937 (tp30) cc_final: 0.7638 (tp30) REVERT: F 144 MET cc_start: 0.8193 (mmm) cc_final: 0.7755 (mpp) REVERT: B 46 ASP cc_start: 0.7511 (t0) cc_final: 0.7105 (t70) REVERT: B 99 MET cc_start: 0.7918 (mtp) cc_final: 0.7714 (mtm) REVERT: B 129 ASN cc_start: 0.9009 (t0) cc_final: 0.8578 (t0) REVERT: B 214 GLN cc_start: 0.8249 (tt0) cc_final: 0.7993 (tm-30) REVERT: B 323 LYS cc_start: 0.8357 (tptp) cc_final: 0.8056 (tppt) REVERT: B 330 CYS cc_start: 0.8281 (m) cc_final: 0.8061 (m) REVERT: B 369 GLN cc_start: 0.7562 (pt0) cc_final: 0.7136 (tt0) REVERT: B 389 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6194 (mt-10) REVERT: B 420 ILE cc_start: 0.8282 (mt) cc_final: 0.8039 (tt) REVERT: B 451 VAL cc_start: 0.9156 (p) cc_final: 0.8938 (t) REVERT: B 474 MET cc_start: 0.7971 (ttp) cc_final: 0.7769 (ttm) REVERT: B 522 GLU cc_start: 0.8000 (mp0) cc_final: 0.7315 (mp0) REVERT: B 623 TYR cc_start: 0.7470 (m-80) cc_final: 0.7085 (m-80) REVERT: C 43 ARG cc_start: 0.8097 (mmt180) cc_final: 0.7371 (mmm-85) REVERT: C 97 LEU cc_start: 0.7438 (mm) cc_final: 0.7030 (mm) REVERT: C 126 MET cc_start: 0.7860 (mmm) cc_final: 0.7628 (mtp) REVERT: C 160 ILE cc_start: 0.8860 (pt) cc_final: 0.8362 (pt) REVERT: C 258 HIS cc_start: 0.8314 (t-90) cc_final: 0.7848 (t-170) REVERT: C 323 LYS cc_start: 0.7967 (tptp) cc_final: 0.7545 (mptt) REVERT: C 328 TYR cc_start: 0.8173 (m-10) cc_final: 0.7846 (m-10) REVERT: C 340 MET cc_start: 0.8595 (mmm) cc_final: 0.8204 (tpp) REVERT: C 365 ILE cc_start: 0.7676 (mt) cc_final: 0.7249 (pt) REVERT: C 383 ASN cc_start: 0.8308 (m-40) cc_final: 0.8003 (m-40) REVERT: C 386 LEU cc_start: 0.8554 (tp) cc_final: 0.8298 (tp) REVERT: C 389 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6775 (mt-10) REVERT: C 489 ASP cc_start: 0.7934 (t70) cc_final: 0.7666 (m-30) REVERT: C 515 GLU cc_start: 0.7960 (tp30) cc_final: 0.7589 (tp30) REVERT: C 516 ASP cc_start: 0.8348 (t0) cc_final: 0.8047 (t0) REVERT: C 546 ASN cc_start: 0.7969 (t0) cc_final: 0.7750 (t0) REVERT: C 570 MET cc_start: 0.8773 (tpp) cc_final: 0.8560 (mmm) REVERT: C 603 MET cc_start: 0.7919 (tmm) cc_final: 0.7531 (tmm) REVERT: C 611 PHE cc_start: 0.6660 (m-10) cc_final: 0.6008 (m-10) REVERT: C 612 LEU cc_start: 0.8815 (mp) cc_final: 0.8067 (mt) REVERT: D 61 LEU cc_start: 0.6951 (mt) cc_final: 0.6460 (mt) REVERT: D 100 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7298 (tt0) REVERT: D 216 TYR cc_start: 0.8075 (t80) cc_final: 0.7379 (t80) REVERT: D 255 MET cc_start: 0.7277 (mmm) cc_final: 0.6717 (mmm) REVERT: D 328 TYR cc_start: 0.8537 (m-10) cc_final: 0.8167 (m-10) REVERT: D 381 GLN cc_start: 0.7056 (mt0) cc_final: 0.6628 (tp40) REVERT: D 402 LEU cc_start: 0.8703 (mt) cc_final: 0.8461 (mt) REVERT: D 555 TYR cc_start: 0.8555 (t80) cc_final: 0.8111 (t80) REVERT: D 580 ASP cc_start: 0.8371 (t70) cc_final: 0.7752 (t0) REVERT: D 621 TYR cc_start: 0.5468 (p90) cc_final: 0.5116 (p90) REVERT: D 629 TRP cc_start: 0.8684 (m100) cc_final: 0.8438 (m100) outliers start: 9 outliers final: 3 residues processed: 791 average time/residue: 0.1627 time to fit residues: 193.8854 Evaluate side-chains 523 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 518 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 389 GLU Chi-restraints excluded: chain C residue 389 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 0.1980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 158 ASN A 310 GLN A 446 ASN A 582 HIS F 3 GLN F 60 ASN B 27 GLN B 158 ASN B 446 ASN B 509 HIS B 513 GLN B 519 ASN B 582 HIS B 636 HIS C 157 HIS C 158 ASN C 446 ASN C 582 HIS D 27 GLN D 51 GLN D 128 GLN D 265 HIS D 446 ASN D 509 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.161603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135741 restraints weight = 32146.273| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 3.02 r_work: 0.3522 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21419 Z= 0.133 Angle : 0.683 10.111 29073 Z= 0.344 Chirality : 0.042 0.167 3307 Planarity : 0.005 0.053 3701 Dihedral : 6.668 108.782 2871 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.18 % Allowed : 18.30 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.14), residues: 2612 helix: -2.53 (0.10), residues: 1504 sheet: -3.37 (0.45), residues: 76 loop : -2.20 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 33 TYR 0.018 0.002 TYR C 555 PHE 0.019 0.001 PHE D 319 TRP 0.020 0.001 TRP B 29 HIS 0.005 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00297 (21419) covalent geometry : angle 0.68340 (29073) hydrogen bonds : bond 0.04148 ( 871) hydrogen bonds : angle 4.79248 ( 2457) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 593 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7734 (mt0) cc_final: 0.7392 (mt0) REVERT: A 34 ASP cc_start: 0.7916 (m-30) cc_final: 0.6614 (m-30) REVERT: A 35 ARG cc_start: 0.8543 (mtt180) cc_final: 0.8183 (mmm-85) REVERT: A 126 MET cc_start: 0.8704 (mmm) cc_final: 0.8130 (mtm) REVERT: A 159 LEU cc_start: 0.9165 (mm) cc_final: 0.8932 (mm) REVERT: A 162 TYR cc_start: 0.8769 (m-10) cc_final: 0.8487 (m-10) REVERT: A 164 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7719 (mt-10) REVERT: A 180 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.8113 (ttm-80) REVERT: A 181 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 188 ASP cc_start: 0.7713 (p0) cc_final: 0.7426 (p0) REVERT: A 230 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8046 (pm20) REVERT: A 288 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 314 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8244 (tttp) REVERT: A 323 LYS cc_start: 0.8582 (tptp) cc_final: 0.8266 (tptt) REVERT: A 418 GLN cc_start: 0.7272 (tp-100) cc_final: 0.6311 (tp40) REVERT: A 442 MET cc_start: 0.8398 (mmm) cc_final: 0.8048 (mmt) REVERT: A 485 MET cc_start: 0.8509 (mmt) cc_final: 0.8209 (mmm) REVERT: A 486 ILE cc_start: 0.9262 (tt) cc_final: 0.9003 (tt) REVERT: A 492 ARG cc_start: 0.8495 (ptp-170) cc_final: 0.7712 (ptp90) REVERT: A 522 GLU cc_start: 0.8799 (mp0) cc_final: 0.8328 (mp0) REVERT: A 553 PHE cc_start: 0.6632 (t80) cc_final: 0.6056 (p90) REVERT: A 637 HIS cc_start: 0.7912 (p-80) cc_final: 0.7568 (p90) REVERT: E 700 ARG cc_start: 0.7520 (ttp-110) cc_final: 0.6942 (ptt90) REVERT: E 703 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6609 (mm-30) REVERT: F 2 ASP cc_start: 0.7108 (t0) cc_final: 0.6626 (t0) REVERT: F 3 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7062 (pp30) REVERT: F 74 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6881 (ttt180) REVERT: F 75 LYS cc_start: 0.7365 (mmtt) cc_final: 0.7098 (mmmt) REVERT: F 86 ARG cc_start: 0.7099 (ttt-90) cc_final: 0.6866 (ttp-170) REVERT: F 109 MET cc_start: 0.9320 (mmt) cc_final: 0.8813 (mmt) REVERT: F 114 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7800 (mt-10) REVERT: F 123 GLU cc_start: 0.7436 (tp30) cc_final: 0.7064 (tp30) REVERT: F 139 GLU cc_start: 0.8159 (tp30) cc_final: 0.7295 (tp30) REVERT: F 144 MET cc_start: 0.8535 (mmm) cc_final: 0.8294 (tpp) REVERT: B 34 ASP cc_start: 0.7729 (m-30) cc_final: 0.7220 (m-30) REVERT: B 99 MET cc_start: 0.7903 (mtp) cc_final: 0.7491 (mtm) REVERT: B 195 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8119 (tt) REVERT: B 214 GLN cc_start: 0.8367 (tt0) cc_final: 0.8156 (tp-100) REVERT: B 216 TYR cc_start: 0.8554 (t80) cc_final: 0.8186 (t80) REVERT: B 474 MET cc_start: 0.8471 (ttp) cc_final: 0.8132 (ttm) REVERT: B 605 GLU cc_start: 0.8600 (tt0) cc_final: 0.8342 (tt0) REVERT: C 40 GLN cc_start: 0.7936 (tt0) cc_final: 0.7695 (tt0) REVERT: C 43 ARG cc_start: 0.8524 (mmt180) cc_final: 0.7777 (mmm-85) REVERT: C 97 LEU cc_start: 0.7451 (mm) cc_final: 0.6958 (mt) REVERT: C 126 MET cc_start: 0.8209 (mmm) cc_final: 0.7606 (mtm) REVERT: C 160 ILE cc_start: 0.8910 (pt) cc_final: 0.8679 (pt) REVERT: C 161 TYR cc_start: 0.8912 (t80) cc_final: 0.7627 (t80) REVERT: C 215 MET cc_start: 0.8565 (tpp) cc_final: 0.8295 (tpp) REVERT: C 242 THR cc_start: 0.8900 (m) cc_final: 0.8634 (t) REVERT: C 250 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8435 (mm-30) REVERT: C 315 GLU cc_start: 0.8123 (mp0) cc_final: 0.7810 (pm20) REVERT: C 328 TYR cc_start: 0.8504 (m-10) cc_final: 0.8270 (m-10) REVERT: C 380 HIS cc_start: 0.8077 (t70) cc_final: 0.7725 (t70) REVERT: C 386 LEU cc_start: 0.8505 (tp) cc_final: 0.8188 (tp) REVERT: C 389 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6733 (tt0) REVERT: C 515 GLU cc_start: 0.8370 (tp30) cc_final: 0.7982 (tp30) REVERT: C 516 ASP cc_start: 0.8735 (t0) cc_final: 0.8343 (t0) REVERT: C 546 ASN cc_start: 0.8215 (t0) cc_final: 0.7850 (t0) REVERT: C 570 MET cc_start: 0.8814 (tpp) cc_final: 0.8261 (mmm) REVERT: C 611 PHE cc_start: 0.7193 (m-10) cc_final: 0.6477 (m-10) REVERT: C 612 LEU cc_start: 0.8883 (mp) cc_final: 0.8255 (mt) REVERT: D 61 LEU cc_start: 0.7036 (mt) cc_final: 0.6324 (mt) REVERT: D 100 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7694 (mm-30) REVERT: D 104 GLU cc_start: 0.7860 (pm20) cc_final: 0.6868 (tp30) REVERT: D 216 TYR cc_start: 0.8382 (t80) cc_final: 0.7399 (t80) REVERT: D 242 THR cc_start: 0.8652 (m) cc_final: 0.8413 (t) REVERT: D 255 MET cc_start: 0.8092 (mmm) cc_final: 0.7408 (mmm) REVERT: D 354 LEU cc_start: 0.7750 (tt) cc_final: 0.7353 (mt) REVERT: D 381 GLN cc_start: 0.7084 (mt0) cc_final: 0.6302 (tm-30) REVERT: D 553 PHE cc_start: 0.7293 (t80) cc_final: 0.6260 (p90) REVERT: D 555 TYR cc_start: 0.8782 (t80) cc_final: 0.8301 (t80) REVERT: D 570 MET cc_start: 0.9099 (mmm) cc_final: 0.8785 (mmm) REVERT: D 580 ASP cc_start: 0.8518 (t70) cc_final: 0.8145 (t0) REVERT: D 591 GLU cc_start: 0.8550 (pt0) cc_final: 0.8304 (pt0) REVERT: D 618 ILE cc_start: 0.8429 (mp) cc_final: 0.8215 (mm) outliers start: 49 outliers final: 20 residues processed: 623 average time/residue: 0.1500 time to fit residues: 145.0926 Evaluate side-chains 529 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 502 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 3 GLN Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 389 GLU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 282 GLU Chi-restraints excluded: chain D residue 451 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 259 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 176 optimal weight: 0.0770 chunk 258 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 191 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 129 ASN F 60 ASN B 118 GLN B 128 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 GLN ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 637 HIS D 31 GLN D 265 HIS ** D 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 ASN D 582 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.161533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135985 restraints weight = 32270.753| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.97 r_work: 0.3516 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 21419 Z= 0.110 Angle : 0.610 9.777 29073 Z= 0.303 Chirality : 0.041 0.161 3307 Planarity : 0.004 0.052 3701 Dihedral : 5.269 114.271 2863 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.29 % Allowed : 19.55 % Favored : 77.17 % 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: -2.38 (0.15), residues: 2612 helix: -1.18 (0.12), residues: 1482 sheet: -3.18 (0.45), residues: 82 loop : -1.86 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 594 TYR 0.017 0.001 TYR C 621 PHE 0.017 0.001 PHE D 319 TRP 0.020 0.001 TRP B 29 HIS 0.011 0.001 HIS D 509 Details of bonding type rmsd covalent geometry : bond 0.00243 (21419) covalent geometry : angle 0.61029 (29073) hydrogen bonds : bond 0.03252 ( 871) hydrogen bonds : angle 4.08831 ( 2457) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 540 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7520 (mt0) cc_final: 0.7254 (mt0) REVERT: A 35 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8164 (mmm-85) REVERT: A 38 MET cc_start: 0.8616 (mtp) cc_final: 0.8351 (mtp) REVERT: A 126 MET cc_start: 0.8778 (mmm) cc_final: 0.8179 (mtm) REVERT: A 159 LEU cc_start: 0.9144 (mm) cc_final: 0.8899 (mm) REVERT: A 162 TYR cc_start: 0.8757 (m-10) cc_final: 0.8452 (m-10) REVERT: A 164 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7737 (mt-10) REVERT: A 180 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8036 (ttm-80) REVERT: A 181 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 188 ASP cc_start: 0.7748 (p0) cc_final: 0.7450 (p0) REVERT: A 230 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: A 257 GLN cc_start: 0.8832 (tp40) cc_final: 0.8522 (tp-100) REVERT: A 288 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7506 (mp0) REVERT: A 295 LEU cc_start: 0.8249 (mt) cc_final: 0.8008 (mp) REVERT: A 296 VAL cc_start: 0.9092 (p) cc_final: 0.8826 (p) REVERT: A 314 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8073 (tttp) REVERT: A 323 LYS cc_start: 0.8459 (tptp) cc_final: 0.8103 (tptt) REVERT: A 359 ARG cc_start: 0.6649 (OUTLIER) cc_final: 0.6090 (ptt-90) REVERT: A 397 VAL cc_start: 0.9055 (OUTLIER) cc_final: 0.8822 (p) REVERT: A 418 GLN cc_start: 0.7174 (tp-100) cc_final: 0.6705 (tp40) REVERT: A 442 MET cc_start: 0.8323 (mmm) cc_final: 0.8117 (mmt) REVERT: A 485 MET cc_start: 0.8390 (mmt) cc_final: 0.8117 (mmm) REVERT: A 486 ILE cc_start: 0.9126 (tt) cc_final: 0.8821 (tt) REVERT: A 492 ARG cc_start: 0.8449 (ptp-170) cc_final: 0.7948 (ptp90) REVERT: A 497 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7395 (tmm) REVERT: A 522 GLU cc_start: 0.8772 (mp0) cc_final: 0.8330 (mp0) REVERT: A 553 PHE cc_start: 0.6568 (t80) cc_final: 0.5922 (p90) REVERT: A 592 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8846 (mp) REVERT: A 637 HIS cc_start: 0.7937 (p-80) cc_final: 0.7595 (p90) REVERT: E 700 ARG cc_start: 0.7483 (ttp-110) cc_final: 0.6676 (ptt90) REVERT: F 2 ASP cc_start: 0.7272 (t0) cc_final: 0.6789 (t0) REVERT: F 74 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6824 (ttt180) REVERT: F 75 LYS cc_start: 0.7458 (mmtt) cc_final: 0.6644 (mmmt) REVERT: F 76 MET cc_start: 0.6807 (mmp) cc_final: 0.6570 (mmm) REVERT: F 86 ARG cc_start: 0.7030 (ttt-90) cc_final: 0.6801 (ttp-170) REVERT: F 109 MET cc_start: 0.9223 (mmt) cc_final: 0.8863 (mmt) REVERT: F 139 GLU cc_start: 0.8094 (tp30) cc_final: 0.7233 (tp30) REVERT: B 34 ASP cc_start: 0.7774 (m-30) cc_final: 0.7297 (m-30) REVERT: B 99 MET cc_start: 0.7986 (mtp) cc_final: 0.7384 (mtm) REVERT: B 126 MET cc_start: 0.8010 (ttm) cc_final: 0.7786 (ttm) REVERT: B 216 TYR cc_start: 0.8569 (t80) cc_final: 0.8289 (t80) REVERT: B 309 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8143 (mp0) REVERT: B 474 MET cc_start: 0.8501 (ttp) cc_final: 0.8099 (ttm) REVERT: C 43 ARG cc_start: 0.8482 (mmt180) cc_final: 0.7751 (mmm-85) REVERT: C 97 LEU cc_start: 0.7489 (mm) cc_final: 0.7061 (mm) REVERT: C 161 TYR cc_start: 0.8897 (t80) cc_final: 0.8617 (t80) REVERT: C 250 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8527 (mm-30) REVERT: C 328 TYR cc_start: 0.8506 (m-10) cc_final: 0.8112 (m-10) REVERT: C 380 HIS cc_start: 0.8178 (t70) cc_final: 0.7812 (t70) REVERT: C 386 LEU cc_start: 0.8548 (tp) cc_final: 0.8206 (tp) REVERT: C 515 GLU cc_start: 0.8389 (tp30) cc_final: 0.7958 (tp30) REVERT: C 516 ASP cc_start: 0.8741 (t0) cc_final: 0.8477 (t0) REVERT: C 525 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7013 (m-30) REVERT: C 546 ASN cc_start: 0.8149 (t0) cc_final: 0.7731 (t0) REVERT: C 612 LEU cc_start: 0.8981 (mp) cc_final: 0.8422 (mt) REVERT: D 61 LEU cc_start: 0.6788 (mt) cc_final: 0.5946 (mt) REVERT: D 100 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7796 (mm-30) REVERT: D 113 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7899 (tp30) REVERT: D 211 PHE cc_start: 0.7990 (m-80) cc_final: 0.7660 (m-80) REVERT: D 216 TYR cc_start: 0.8337 (t80) cc_final: 0.7531 (t80) REVERT: D 230 GLN cc_start: 0.8062 (pm20) cc_final: 0.7842 (pm20) REVERT: D 234 LEU cc_start: 0.8064 (mp) cc_final: 0.7582 (tt) REVERT: D 255 MET cc_start: 0.8165 (mmm) cc_final: 0.7496 (mmm) REVERT: D 257 GLN cc_start: 0.8179 (mt0) cc_final: 0.7865 (tm-30) REVERT: D 354 LEU cc_start: 0.7731 (tt) cc_final: 0.7328 (mt) REVERT: D 381 GLN cc_start: 0.7048 (mt0) cc_final: 0.6195 (tm-30) REVERT: D 485 MET cc_start: 0.8394 (mmt) cc_final: 0.7845 (mmm) REVERT: D 495 TRP cc_start: 0.8860 (m100) cc_final: 0.8624 (m100) REVERT: D 553 PHE cc_start: 0.7474 (t80) cc_final: 0.6165 (p90) REVERT: D 580 ASP cc_start: 0.8419 (t70) cc_final: 0.8005 (t0) REVERT: D 618 ILE cc_start: 0.8344 (mp) cc_final: 0.8066 (mm) outliers start: 74 outliers final: 37 residues processed: 580 average time/residue: 0.1434 time to fit residues: 130.7456 Evaluate side-chains 528 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 482 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 497 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 623 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 259 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 ASN A 546 ASN B 358 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 513 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.149843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123910 restraints weight = 32216.995| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.97 r_work: 0.3238 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21419 Z= 0.145 Angle : 0.624 9.675 29073 Z= 0.310 Chirality : 0.042 0.169 3307 Planarity : 0.004 0.045 3701 Dihedral : 4.607 28.084 2860 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.38 % Allowed : 21.46 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2612 helix: -0.43 (0.13), residues: 1484 sheet: -3.25 (0.46), residues: 82 loop : -1.68 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 75 TYR 0.023 0.001 TYR C 621 PHE 0.018 0.001 PHE D 319 TRP 0.034 0.001 TRP C 29 HIS 0.006 0.001 HIS D 509 Details of bonding type rmsd covalent geometry : bond 0.00336 (21419) covalent geometry : angle 0.62401 (29073) hydrogen bonds : bond 0.03118 ( 871) hydrogen bonds : angle 4.00906 ( 2457) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 509 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7595 (mt0) cc_final: 0.7374 (mt0) REVERT: A 33 ARG cc_start: 0.7730 (mmm-85) cc_final: 0.6944 (tpt-90) REVERT: A 35 ARG cc_start: 0.8570 (mtt180) cc_final: 0.8308 (mmm-85) REVERT: A 126 MET cc_start: 0.8775 (mmm) cc_final: 0.8194 (mtm) REVERT: A 159 LEU cc_start: 0.9136 (mm) cc_final: 0.8871 (mm) REVERT: A 162 TYR cc_start: 0.8796 (m-10) cc_final: 0.8496 (m-10) REVERT: A 180 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.8052 (ttm-80) REVERT: A 181 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7953 (mp) REVERT: A 188 ASP cc_start: 0.7723 (p0) cc_final: 0.7453 (p0) REVERT: A 252 ASN cc_start: 0.8996 (t0) cc_final: 0.8314 (t0) REVERT: A 288 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: A 294 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: A 314 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8160 (tttp) REVERT: A 323 LYS cc_start: 0.8518 (tptp) cc_final: 0.8161 (tptt) REVERT: A 359 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5670 (ptt-90) REVERT: A 382 ASP cc_start: 0.7372 (m-30) cc_final: 0.6786 (m-30) REVERT: A 397 VAL cc_start: 0.9133 (p) cc_final: 0.8902 (p) REVERT: A 418 GLN cc_start: 0.7452 (tp-100) cc_final: 0.6988 (tp40) REVERT: A 485 MET cc_start: 0.8492 (mmt) cc_final: 0.8226 (mmm) REVERT: A 486 ILE cc_start: 0.9273 (tt) cc_final: 0.8968 (tt) REVERT: A 522 GLU cc_start: 0.8800 (mp0) cc_final: 0.8401 (mp0) REVERT: A 546 ASN cc_start: 0.8398 (t0) cc_final: 0.7897 (t0) REVERT: A 553 PHE cc_start: 0.6577 (t80) cc_final: 0.6005 (p90) REVERT: A 637 HIS cc_start: 0.7968 (p-80) cc_final: 0.7642 (p90) REVERT: F 2 ASP cc_start: 0.7171 (t0) cc_final: 0.6786 (t0) REVERT: F 7 GLU cc_start: 0.8460 (pm20) cc_final: 0.7999 (mm-30) REVERT: F 14 GLU cc_start: 0.7860 (tt0) cc_final: 0.7584 (tt0) REVERT: F 74 ARG cc_start: 0.7265 (OUTLIER) cc_final: 0.6781 (ttt180) REVERT: F 75 LYS cc_start: 0.7675 (mmtt) cc_final: 0.6803 (mmmt) REVERT: F 76 MET cc_start: 0.6783 (mmp) cc_final: 0.6574 (mmm) REVERT: F 139 GLU cc_start: 0.8168 (tp30) cc_final: 0.7299 (tp30) REVERT: B 46 ASP cc_start: 0.7951 (m-30) cc_final: 0.7745 (m-30) REVERT: B 99 MET cc_start: 0.7989 (mtp) cc_final: 0.7535 (mtm) REVERT: B 195 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8226 (tt) REVERT: B 211 PHE cc_start: 0.7923 (m-80) cc_final: 0.7710 (m-80) REVERT: B 406 ASP cc_start: 0.8972 (m-30) cc_final: 0.8729 (m-30) REVERT: B 474 MET cc_start: 0.8481 (ttp) cc_final: 0.8120 (ttm) REVERT: B 634 GLU cc_start: 0.7860 (pt0) cc_final: 0.7640 (pt0) REVERT: C 43 ARG cc_start: 0.8550 (mmt180) cc_final: 0.7904 (mmm-85) REVERT: C 97 LEU cc_start: 0.7457 (mm) cc_final: 0.7032 (mm) REVERT: C 126 MET cc_start: 0.8402 (mmm) cc_final: 0.7922 (mtm) REVERT: C 161 TYR cc_start: 0.9006 (t80) cc_final: 0.8310 (t80) REVERT: C 250 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8700 (mm-30) REVERT: C 328 TYR cc_start: 0.8524 (m-10) cc_final: 0.8149 (m-10) REVERT: C 381 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6503 (mm110) REVERT: C 386 LEU cc_start: 0.8612 (tp) cc_final: 0.8283 (tp) REVERT: C 497 MET cc_start: 0.8590 (tpt) cc_final: 0.8244 (tpt) REVERT: C 525 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7161 (m-30) REVERT: C 537 PHE cc_start: 0.8929 (t80) cc_final: 0.8187 (t80) REVERT: C 546 ASN cc_start: 0.8203 (t0) cc_final: 0.7833 (t0) REVERT: C 554 MET cc_start: 0.8060 (tpp) cc_final: 0.7799 (tpp) REVERT: C 612 LEU cc_start: 0.9125 (mp) cc_final: 0.8305 (mt) REVERT: C 618 ILE cc_start: 0.8672 (mp) cc_final: 0.8429 (mm) REVERT: D 61 LEU cc_start: 0.7011 (mt) cc_final: 0.6117 (mt) REVERT: D 100 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 113 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8042 (tp30) REVERT: D 211 PHE cc_start: 0.8072 (m-80) cc_final: 0.7783 (m-80) REVERT: D 230 GLN cc_start: 0.8121 (pm20) cc_final: 0.7807 (pm20) REVERT: D 255 MET cc_start: 0.8274 (mmm) cc_final: 0.7841 (mmp) REVERT: D 257 GLN cc_start: 0.8228 (mt0) cc_final: 0.7876 (tm-30) REVERT: D 301 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7128 (ttmm) REVERT: D 328 TYR cc_start: 0.8730 (m-10) cc_final: 0.8346 (m-80) REVERT: D 354 LEU cc_start: 0.7841 (tt) cc_final: 0.7357 (mt) REVERT: D 381 GLN cc_start: 0.7160 (mt0) cc_final: 0.6387 (tm-30) REVERT: D 495 TRP cc_start: 0.8927 (m100) cc_final: 0.8724 (m100) REVERT: D 501 ILE cc_start: 0.7936 (pt) cc_final: 0.7725 (mt) REVERT: D 553 PHE cc_start: 0.7551 (t80) cc_final: 0.6305 (p90) REVERT: D 580 ASP cc_start: 0.8539 (t70) cc_final: 0.8154 (t0) REVERT: D 603 MET cc_start: 0.8427 (tmm) cc_final: 0.8196 (tmm) outliers start: 76 outliers final: 42 residues processed: 554 average time/residue: 0.1433 time to fit residues: 123.5127 Evaluate side-chains 517 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 468 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 359 ARG Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 557 ILE Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 525 ASP Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 344 THR Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 499 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 225 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 196 optimal weight: 0.0770 chunk 197 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 358 ASN ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 HIS C 310 GLN C 637 HIS D 519 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.153597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127729 restraints weight = 31724.258| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.97 r_work: 0.3236 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21419 Z= 0.103 Angle : 0.590 9.132 29073 Z= 0.289 Chirality : 0.040 0.153 3307 Planarity : 0.003 0.047 3701 Dihedral : 4.388 28.655 2860 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.93 % Allowed : 21.95 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.17), residues: 2612 helix: 0.09 (0.13), residues: 1508 sheet: -3.10 (0.48), residues: 77 loop : -1.47 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 414 TYR 0.019 0.001 TYR A 415 PHE 0.022 0.001 PHE D 319 TRP 0.027 0.001 TRP C 29 HIS 0.003 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00229 (21419) covalent geometry : angle 0.58961 (29073) hydrogen bonds : bond 0.02759 ( 871) hydrogen bonds : angle 3.77051 ( 2457) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 533 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7329 (tpp80) REVERT: A 35 ARG cc_start: 0.8505 (mtt180) cc_final: 0.8284 (mmm-85) REVERT: A 126 MET cc_start: 0.8685 (mmm) cc_final: 0.8142 (mtm) REVERT: A 159 LEU cc_start: 0.9056 (mm) cc_final: 0.8805 (mm) REVERT: A 162 TYR cc_start: 0.8810 (m-10) cc_final: 0.8406 (m-10) REVERT: A 181 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 188 ASP cc_start: 0.7647 (p0) cc_final: 0.7416 (p0) REVERT: A 252 ASN cc_start: 0.8918 (t0) cc_final: 0.8296 (t0) REVERT: A 257 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8401 (tp-100) REVERT: A 288 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: A 295 LEU cc_start: 0.8342 (mt) cc_final: 0.8104 (mp) REVERT: A 314 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8143 (tttp) REVERT: A 355 ARG cc_start: 0.5913 (OUTLIER) cc_final: 0.5474 (tmm-80) REVERT: A 382 ASP cc_start: 0.7358 (m-30) cc_final: 0.6805 (m-30) REVERT: A 397 VAL cc_start: 0.9085 (OUTLIER) cc_final: 0.8861 (p) REVERT: A 442 MET cc_start: 0.8460 (mmt) cc_final: 0.8083 (mmt) REVERT: A 485 MET cc_start: 0.8475 (mmt) cc_final: 0.8186 (mmm) REVERT: A 486 ILE cc_start: 0.9206 (tt) cc_final: 0.8903 (tt) REVERT: A 497 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7383 (ttp) REVERT: A 522 GLU cc_start: 0.8744 (mp0) cc_final: 0.8438 (mp0) REVERT: A 546 ASN cc_start: 0.8304 (t0) cc_final: 0.7794 (t0) REVERT: A 553 PHE cc_start: 0.6517 (t80) cc_final: 0.5876 (p90) REVERT: A 592 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8930 (mp) REVERT: A 622 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7634 (tm-30) REVERT: A 637 HIS cc_start: 0.7878 (p-80) cc_final: 0.7541 (p90) REVERT: F 2 ASP cc_start: 0.7254 (t0) cc_final: 0.6826 (t0) REVERT: F 14 GLU cc_start: 0.7814 (tt0) cc_final: 0.7608 (tt0) REVERT: F 74 ARG cc_start: 0.7297 (OUTLIER) cc_final: 0.6918 (ttt180) REVERT: F 75 LYS cc_start: 0.7641 (mmtt) cc_final: 0.6783 (mmtp) REVERT: F 76 MET cc_start: 0.6811 (mmp) cc_final: 0.6608 (mmm) REVERT: F 139 GLU cc_start: 0.8185 (tp30) cc_final: 0.7633 (tp30) REVERT: F 143 GLN cc_start: 0.8451 (mt0) cc_final: 0.8202 (tt0) REVERT: B 34 ASP cc_start: 0.7786 (m-30) cc_final: 0.7377 (m-30) REVERT: B 99 MET cc_start: 0.7947 (mtp) cc_final: 0.7506 (mtm) REVERT: B 309 GLU cc_start: 0.8520 (mm-30) cc_final: 0.6748 (tm-30) REVERT: B 406 ASP cc_start: 0.9016 (m-30) cc_final: 0.8746 (m-30) REVERT: B 474 MET cc_start: 0.8470 (ttp) cc_final: 0.8141 (ttm) REVERT: B 554 MET cc_start: 0.8014 (tpp) cc_final: 0.7706 (tpp) REVERT: C 43 ARG cc_start: 0.8545 (mmt180) cc_final: 0.7907 (mmm-85) REVERT: C 97 LEU cc_start: 0.7496 (mm) cc_final: 0.7089 (mm) REVERT: C 126 MET cc_start: 0.8446 (mmm) cc_final: 0.7954 (mtm) REVERT: C 250 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8740 (mm-30) REVERT: C 328 TYR cc_start: 0.8439 (m-10) cc_final: 0.8152 (m-10) REVERT: C 340 MET cc_start: 0.9069 (mmm) cc_final: 0.7986 (tpp) REVERT: C 371 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7990 (ptpp) REVERT: C 381 GLN cc_start: 0.7215 (mm-40) cc_final: 0.6734 (mm-40) REVERT: C 382 ASP cc_start: 0.8369 (m-30) cc_final: 0.8003 (t0) REVERT: C 386 LEU cc_start: 0.8598 (tp) cc_final: 0.8348 (tp) REVERT: C 546 ASN cc_start: 0.8104 (t0) cc_final: 0.7742 (t0) REVERT: C 612 LEU cc_start: 0.9125 (mp) cc_final: 0.8302 (mt) REVERT: C 618 ILE cc_start: 0.8547 (mp) cc_final: 0.8311 (mm) REVERT: C 619 CYS cc_start: 0.6415 (t) cc_final: 0.5888 (t) REVERT: D 61 LEU cc_start: 0.7112 (mt) cc_final: 0.6270 (mt) REVERT: D 100 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7707 (mm-30) REVERT: D 113 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7925 (tp30) REVERT: D 162 TYR cc_start: 0.7892 (m-10) cc_final: 0.7095 (m-10) REVERT: D 216 TYR cc_start: 0.8325 (t80) cc_final: 0.7573 (t80) REVERT: D 255 MET cc_start: 0.8233 (mmm) cc_final: 0.7495 (mmp) REVERT: D 257 GLN cc_start: 0.8334 (mt0) cc_final: 0.7894 (tm-30) REVERT: D 301 LYS cc_start: 0.7619 (ttmm) cc_final: 0.7122 (ttmm) REVERT: D 328 TYR cc_start: 0.8761 (m-10) cc_final: 0.8361 (m-80) REVERT: D 340 MET cc_start: 0.8842 (tpp) cc_final: 0.8377 (tpp) REVERT: D 354 LEU cc_start: 0.7745 (tt) cc_final: 0.7367 (mt) REVERT: D 381 GLN cc_start: 0.7201 (mt0) cc_final: 0.6694 (pp30) REVERT: D 406 ASP cc_start: 0.8428 (m-30) cc_final: 0.7580 (m-30) REVERT: D 495 TRP cc_start: 0.8927 (m100) cc_final: 0.8709 (m100) REVERT: D 555 TYR cc_start: 0.8863 (t80) cc_final: 0.8573 (t80) REVERT: D 580 ASP cc_start: 0.8446 (t70) cc_final: 0.8094 (t0) REVERT: D 587 GLN cc_start: 0.8562 (tt0) cc_final: 0.7914 (tm-30) REVERT: D 603 MET cc_start: 0.8185 (tmm) cc_final: 0.7973 (tmm) outliers start: 66 outliers final: 35 residues processed: 576 average time/residue: 0.1482 time to fit residues: 132.6354 Evaluate side-chains 527 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 484 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 99 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 182 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 127 optimal weight: 0.5980 chunk 157 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 208 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 370 GLN B 519 ASN D 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.132624 restraints weight = 32211.655| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.00 r_work: 0.3435 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21419 Z= 0.120 Angle : 0.596 10.633 29073 Z= 0.294 Chirality : 0.041 0.173 3307 Planarity : 0.004 0.061 3701 Dihedral : 4.352 32.608 2860 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.11 % Allowed : 22.39 % Favored : 74.50 % 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: -0.61 (0.17), residues: 2612 helix: 0.38 (0.14), residues: 1519 sheet: -2.89 (0.51), residues: 77 loop : -1.33 (0.21), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 615 TYR 0.018 0.001 TYR A 415 PHE 0.014 0.001 PHE B 537 TRP 0.026 0.001 TRP C 29 HIS 0.017 0.001 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00280 (21419) covalent geometry : angle 0.59588 (29073) hydrogen bonds : bond 0.02807 ( 871) hydrogen bonds : angle 3.78739 ( 2457) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 501 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7369 (tpp80) REVERT: A 34 ASP cc_start: 0.7804 (m-30) cc_final: 0.7157 (m-30) REVERT: A 35 ARG cc_start: 0.8497 (mtt180) cc_final: 0.8271 (mmm-85) REVERT: A 126 MET cc_start: 0.8717 (mmm) cc_final: 0.8162 (mtm) REVERT: A 159 LEU cc_start: 0.9069 (mm) cc_final: 0.8820 (mm) REVERT: A 162 TYR cc_start: 0.8795 (m-10) cc_final: 0.8475 (m-10) REVERT: A 180 ARG cc_start: 0.8334 (mtt-85) cc_final: 0.8008 (ttm-80) REVERT: A 181 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7839 (mp) REVERT: A 188 ASP cc_start: 0.7646 (p0) cc_final: 0.7419 (p0) REVERT: A 252 ASN cc_start: 0.8959 (t0) cc_final: 0.8298 (t0) REVERT: A 257 GLN cc_start: 0.8693 (tp-100) cc_final: 0.8336 (tp40) REVERT: A 260 MET cc_start: 0.8216 (mmt) cc_final: 0.7879 (mmt) REVERT: A 288 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: A 295 LEU cc_start: 0.8326 (mt) cc_final: 0.8068 (mp) REVERT: A 314 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8195 (tttp) REVERT: A 355 ARG cc_start: 0.5904 (OUTLIER) cc_final: 0.5437 (tmm-80) REVERT: A 369 GLN cc_start: 0.7408 (tp40) cc_final: 0.7067 (tp40) REVERT: A 382 ASP cc_start: 0.7405 (m-30) cc_final: 0.6852 (m-30) REVERT: A 397 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8862 (p) REVERT: A 442 MET cc_start: 0.8423 (mmt) cc_final: 0.8104 (mmt) REVERT: A 485 MET cc_start: 0.8517 (mmt) cc_final: 0.8260 (mmm) REVERT: A 486 ILE cc_start: 0.9210 (tt) cc_final: 0.8939 (tt) REVERT: A 497 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7383 (ttp) REVERT: A 522 GLU cc_start: 0.8743 (mp0) cc_final: 0.8365 (mp0) REVERT: A 546 ASN cc_start: 0.8418 (t0) cc_final: 0.7918 (t0) REVERT: A 553 PHE cc_start: 0.6576 (t80) cc_final: 0.5938 (p90) REVERT: A 622 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7740 (tm-30) REVERT: A 623 TYR cc_start: 0.7978 (m-80) cc_final: 0.7432 (m-80) REVERT: A 637 HIS cc_start: 0.7992 (p-80) cc_final: 0.7672 (p90) REVERT: E 703 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7044 (mm-30) REVERT: F 2 ASP cc_start: 0.7389 (t0) cc_final: 0.7005 (t0) REVERT: F 14 GLU cc_start: 0.7864 (tt0) cc_final: 0.7637 (tt0) REVERT: F 74 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.6810 (ttt180) REVERT: F 75 LYS cc_start: 0.7583 (mmtt) cc_final: 0.6772 (mmtp) REVERT: F 127 GLU cc_start: 0.8545 (tt0) cc_final: 0.7999 (tt0) REVERT: F 139 GLU cc_start: 0.8126 (tp30) cc_final: 0.7653 (tp30) REVERT: B 99 MET cc_start: 0.8006 (mtp) cc_final: 0.7522 (mtm) REVERT: B 294 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7949 (tt0) REVERT: B 309 GLU cc_start: 0.8524 (mm-30) cc_final: 0.6830 (tm-30) REVERT: B 406 ASP cc_start: 0.9033 (m-30) cc_final: 0.8760 (m-30) REVERT: B 474 MET cc_start: 0.8475 (ttp) cc_final: 0.8116 (ttm) REVERT: B 554 MET cc_start: 0.8015 (tpp) cc_final: 0.7719 (tpp) REVERT: C 43 ARG cc_start: 0.8521 (mmt180) cc_final: 0.7851 (mmm-85) REVERT: C 97 LEU cc_start: 0.7494 (mm) cc_final: 0.7087 (mm) REVERT: C 126 MET cc_start: 0.8483 (mmm) cc_final: 0.8127 (mtp) REVERT: C 161 TYR cc_start: 0.8985 (t80) cc_final: 0.8425 (t80) REVERT: C 250 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8598 (mm-30) REVERT: C 328 TYR cc_start: 0.8458 (m-10) cc_final: 0.8105 (m-10) REVERT: C 340 MET cc_start: 0.9105 (mmm) cc_final: 0.8041 (tpp) REVERT: C 371 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8026 (ptpp) REVERT: C 381 GLN cc_start: 0.7256 (mm-40) cc_final: 0.6650 (mm110) REVERT: C 382 ASP cc_start: 0.8429 (m-30) cc_final: 0.8028 (t0) REVERT: C 386 LEU cc_start: 0.8600 (tp) cc_final: 0.8349 (tp) REVERT: C 546 ASN cc_start: 0.8164 (t0) cc_final: 0.7764 (t0) REVERT: D 100 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7607 (tt0) REVERT: D 113 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7977 (tp30) REVERT: D 162 TYR cc_start: 0.7989 (m-10) cc_final: 0.7158 (m-10) REVERT: D 216 TYR cc_start: 0.8366 (t80) cc_final: 0.7532 (t80) REVERT: D 252 ASN cc_start: 0.8837 (t0) cc_final: 0.8407 (t0) REVERT: D 255 MET cc_start: 0.8190 (mmm) cc_final: 0.7690 (mmp) REVERT: D 257 GLN cc_start: 0.8249 (mt0) cc_final: 0.7852 (tm-30) REVERT: D 301 LYS cc_start: 0.7725 (ttmm) cc_final: 0.7207 (ttmm) REVERT: D 328 TYR cc_start: 0.8844 (m-10) cc_final: 0.8375 (m-80) REVERT: D 381 GLN cc_start: 0.7252 (mt0) cc_final: 0.6687 (pp30) REVERT: D 406 ASP cc_start: 0.8499 (m-30) cc_final: 0.7655 (m-30) REVERT: D 580 ASP cc_start: 0.8529 (t70) cc_final: 0.8185 (t0) REVERT: D 587 GLN cc_start: 0.8614 (tt0) cc_final: 0.7925 (tm-30) REVERT: D 603 MET cc_start: 0.8132 (tmm) cc_final: 0.7919 (tmm) outliers start: 70 outliers final: 50 residues processed: 543 average time/residue: 0.1397 time to fit residues: 119.7918 Evaluate side-chains 538 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 481 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 613 TRP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 613 TRP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 25 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 44 optimal weight: 0.3980 chunk 225 optimal weight: 0.7980 chunk 134 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN C 238 HIS D 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.159845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.134029 restraints weight = 32313.204| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.07 r_work: 0.3467 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21419 Z= 0.108 Angle : 0.590 9.661 29073 Z= 0.291 Chirality : 0.041 0.167 3307 Planarity : 0.003 0.041 3701 Dihedral : 4.290 36.993 2860 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.98 % Allowed : 22.97 % Favored : 74.06 % 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: -0.36 (0.17), residues: 2612 helix: 0.58 (0.14), residues: 1518 sheet: -2.84 (0.52), residues: 77 loop : -1.21 (0.21), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 305 TYR 0.018 0.001 TYR A 415 PHE 0.018 0.001 PHE F 68 TRP 0.024 0.001 TRP C 29 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00245 (21419) covalent geometry : angle 0.59038 (29073) hydrogen bonds : bond 0.02732 ( 871) hydrogen bonds : angle 3.70645 ( 2457) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 505 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7685 (mmm-85) cc_final: 0.7380 (tpp80) REVERT: A 34 ASP cc_start: 0.7732 (m-30) cc_final: 0.7122 (m-30) REVERT: A 35 ARG cc_start: 0.8463 (mtt180) cc_final: 0.8226 (mmm-85) REVERT: A 46 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7714 (t0) REVERT: A 126 MET cc_start: 0.8716 (mmm) cc_final: 0.8165 (mtm) REVERT: A 162 TYR cc_start: 0.8739 (m-10) cc_final: 0.8372 (m-10) REVERT: A 180 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7984 (ttm-80) REVERT: A 181 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7867 (mp) REVERT: A 188 ASP cc_start: 0.7565 (p0) cc_final: 0.7357 (p0) REVERT: A 252 ASN cc_start: 0.8920 (t0) cc_final: 0.8275 (t0) REVERT: A 257 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8281 (tp40) REVERT: A 260 MET cc_start: 0.8166 (mmt) cc_final: 0.7914 (mmt) REVERT: A 288 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: A 295 LEU cc_start: 0.8312 (mt) cc_final: 0.8074 (mp) REVERT: A 314 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8149 (tttp) REVERT: A 355 ARG cc_start: 0.5938 (OUTLIER) cc_final: 0.5529 (tmm-80) REVERT: A 382 ASP cc_start: 0.7405 (m-30) cc_final: 0.6865 (m-30) REVERT: A 397 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8847 (p) REVERT: A 442 MET cc_start: 0.8366 (mmt) cc_final: 0.8128 (mmt) REVERT: A 485 MET cc_start: 0.8550 (mmt) cc_final: 0.8308 (mmm) REVERT: A 486 ILE cc_start: 0.9152 (tt) cc_final: 0.8863 (tt) REVERT: A 497 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7383 (ttp) REVERT: A 546 ASN cc_start: 0.8411 (t0) cc_final: 0.7911 (t0) REVERT: A 553 PHE cc_start: 0.6696 (t80) cc_final: 0.5839 (p90) REVERT: A 570 MET cc_start: 0.9064 (tpp) cc_final: 0.8125 (mmt) REVERT: A 622 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7840 (tm-30) REVERT: A 623 TYR cc_start: 0.7920 (m-80) cc_final: 0.7204 (m-80) REVERT: A 637 HIS cc_start: 0.7989 (p-80) cc_final: 0.7719 (p-80) REVERT: F 2 ASP cc_start: 0.7336 (t0) cc_final: 0.6961 (t0) REVERT: F 14 GLU cc_start: 0.7855 (tt0) cc_final: 0.7646 (tt0) REVERT: F 75 LYS cc_start: 0.7505 (mmtt) cc_final: 0.6893 (mmtm) REVERT: F 76 MET cc_start: 0.7117 (mmm) cc_final: 0.6869 (mmm) REVERT: F 127 GLU cc_start: 0.8182 (tt0) cc_final: 0.7796 (tt0) REVERT: B 99 MET cc_start: 0.8006 (mtp) cc_final: 0.7573 (mtm) REVERT: B 262 LYS cc_start: 0.8475 (mmmt) cc_final: 0.8207 (tmtt) REVERT: B 294 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7953 (tt0) REVERT: B 309 GLU cc_start: 0.8540 (mm-30) cc_final: 0.6757 (tm-30) REVERT: B 406 ASP cc_start: 0.9046 (m-30) cc_final: 0.8770 (m-30) REVERT: B 474 MET cc_start: 0.8429 (ttp) cc_final: 0.8091 (ttm) REVERT: B 485 MET cc_start: 0.8639 (ttm) cc_final: 0.8340 (mtp) REVERT: B 554 MET cc_start: 0.7982 (tpp) cc_final: 0.7698 (tpp) REVERT: C 43 ARG cc_start: 0.8522 (mmt180) cc_final: 0.7853 (mmm-85) REVERT: C 97 LEU cc_start: 0.7479 (mm) cc_final: 0.7078 (mm) REVERT: C 126 MET cc_start: 0.8508 (mmm) cc_final: 0.8152 (mtp) REVERT: C 161 TYR cc_start: 0.8979 (t80) cc_final: 0.8504 (t80) REVERT: C 328 TYR cc_start: 0.8399 (m-10) cc_final: 0.8069 (m-10) REVERT: C 340 MET cc_start: 0.9087 (mmm) cc_final: 0.8003 (tpp) REVERT: C 371 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7916 (ptpp) REVERT: C 381 GLN cc_start: 0.7258 (mm-40) cc_final: 0.6716 (mm110) REVERT: C 386 LEU cc_start: 0.8583 (tp) cc_final: 0.8356 (tp) REVERT: C 442 MET cc_start: 0.7514 (mmt) cc_final: 0.7230 (mtt) REVERT: C 546 ASN cc_start: 0.8136 (t0) cc_final: 0.7720 (t0) REVERT: C 619 CYS cc_start: 0.5890 (t) cc_final: 0.5165 (t) REVERT: C 628 ARG cc_start: 0.7663 (mtm110) cc_final: 0.7327 (mtm110) REVERT: D 100 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7635 (tt0) REVERT: D 162 TYR cc_start: 0.7909 (m-10) cc_final: 0.7141 (m-10) REVERT: D 211 PHE cc_start: 0.7908 (m-80) cc_final: 0.7554 (m-80) REVERT: D 216 TYR cc_start: 0.8385 (t80) cc_final: 0.7546 (t80) REVERT: D 252 ASN cc_start: 0.8795 (t0) cc_final: 0.8352 (t0) REVERT: D 255 MET cc_start: 0.8166 (mmm) cc_final: 0.7668 (mmp) REVERT: D 328 TYR cc_start: 0.8866 (m-10) cc_final: 0.8389 (m-80) REVERT: D 381 GLN cc_start: 0.7065 (mt0) cc_final: 0.6531 (pp30) REVERT: D 406 ASP cc_start: 0.8453 (m-30) cc_final: 0.7636 (m-30) REVERT: D 580 ASP cc_start: 0.8471 (t70) cc_final: 0.8127 (t0) REVERT: D 587 GLN cc_start: 0.8614 (tt0) cc_final: 0.7951 (tm-30) REVERT: D 603 MET cc_start: 0.8100 (tmm) cc_final: 0.7885 (tmm) REVERT: D 634 GLU cc_start: 0.8513 (tt0) cc_final: 0.7958 (tt0) outliers start: 67 outliers final: 50 residues processed: 545 average time/residue: 0.1351 time to fit residues: 116.2169 Evaluate side-chains 539 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 482 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain C residue 238 HIS Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 448 ASN Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 222 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 246 optimal weight: 2.9990 chunk 102 optimal weight: 0.0040 chunk 53 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 129 ASN C 118 GLN ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.160017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.134339 restraints weight = 32114.576| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 3.07 r_work: 0.3471 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21419 Z= 0.109 Angle : 0.594 9.047 29073 Z= 0.292 Chirality : 0.041 0.157 3307 Planarity : 0.003 0.053 3701 Dihedral : 4.247 41.946 2860 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.15 % Allowed : 23.28 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.17), residues: 2612 helix: 0.73 (0.14), residues: 1507 sheet: -2.83 (0.51), residues: 77 loop : -1.20 (0.21), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 414 TYR 0.017 0.001 TYR A 415 PHE 0.026 0.001 PHE A 534 TRP 0.022 0.001 TRP C 29 HIS 0.016 0.001 HIS C 238 Details of bonding type rmsd covalent geometry : bond 0.00250 (21419) covalent geometry : angle 0.59377 (29073) hydrogen bonds : bond 0.02701 ( 871) hydrogen bonds : angle 3.68165 ( 2457) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 497 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7322 (tpp80) REVERT: A 35 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8225 (mmm-85) REVERT: A 46 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7679 (t0) REVERT: A 126 MET cc_start: 0.8716 (mmm) cc_final: 0.8145 (mtm) REVERT: A 162 TYR cc_start: 0.8691 (m-10) cc_final: 0.8222 (m-10) REVERT: A 180 ARG cc_start: 0.8305 (mtt-85) cc_final: 0.8015 (ttm-80) REVERT: A 181 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7774 (mp) REVERT: A 252 ASN cc_start: 0.8912 (t0) cc_final: 0.8283 (t0) REVERT: A 257 GLN cc_start: 0.8680 (tp-100) cc_final: 0.8290 (tp40) REVERT: A 260 MET cc_start: 0.8150 (mmt) cc_final: 0.7948 (mmt) REVERT: A 288 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 296 VAL cc_start: 0.9307 (p) cc_final: 0.9051 (p) REVERT: A 314 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8142 (tttp) REVERT: A 355 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.5622 (tmm-80) REVERT: A 382 ASP cc_start: 0.7394 (m-30) cc_final: 0.6857 (m-30) REVERT: A 397 VAL cc_start: 0.9064 (OUTLIER) cc_final: 0.8845 (p) REVERT: A 485 MET cc_start: 0.8541 (mmt) cc_final: 0.8275 (mmm) REVERT: A 486 ILE cc_start: 0.9147 (tt) cc_final: 0.8857 (tt) REVERT: A 497 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7402 (ttp) REVERT: A 546 ASN cc_start: 0.8385 (t0) cc_final: 0.7874 (t0) REVERT: A 553 PHE cc_start: 0.6707 (t80) cc_final: 0.5843 (p90) REVERT: A 570 MET cc_start: 0.9029 (tpp) cc_final: 0.8026 (mmt) REVERT: A 592 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8888 (mp) REVERT: A 623 TYR cc_start: 0.7906 (m-80) cc_final: 0.7272 (m-80) REVERT: A 637 HIS cc_start: 0.7975 (p-80) cc_final: 0.7716 (p-80) REVERT: F 2 ASP cc_start: 0.7353 (t0) cc_final: 0.6986 (t0) REVERT: F 14 GLU cc_start: 0.7873 (tt0) cc_final: 0.7663 (tt0) REVERT: F 75 LYS cc_start: 0.7465 (mmtt) cc_final: 0.6926 (mmtm) REVERT: F 76 MET cc_start: 0.7109 (mmm) cc_final: 0.6862 (mmm) REVERT: B 99 MET cc_start: 0.8039 (mtp) cc_final: 0.7603 (mtm) REVERT: B 262 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8209 (tmtt) REVERT: B 294 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7945 (tt0) REVERT: B 309 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7218 (tt0) REVERT: B 406 ASP cc_start: 0.9041 (m-30) cc_final: 0.8772 (m-30) REVERT: B 474 MET cc_start: 0.8421 (ttp) cc_final: 0.8081 (ttm) REVERT: B 485 MET cc_start: 0.8552 (ttm) cc_final: 0.8189 (mtp) REVERT: B 554 MET cc_start: 0.8028 (tpp) cc_final: 0.7758 (tpp) REVERT: C 43 ARG cc_start: 0.8559 (mmt180) cc_final: 0.7874 (mmm-85) REVERT: C 46 ASP cc_start: 0.7935 (m-30) cc_final: 0.7718 (m-30) REVERT: C 97 LEU cc_start: 0.7472 (mm) cc_final: 0.7066 (mm) REVERT: C 126 MET cc_start: 0.8535 (mmm) cc_final: 0.8179 (mtp) REVERT: C 161 TYR cc_start: 0.8945 (t80) cc_final: 0.8523 (t80) REVERT: C 328 TYR cc_start: 0.8355 (m-10) cc_final: 0.8060 (m-10) REVERT: C 340 MET cc_start: 0.9108 (mmm) cc_final: 0.8030 (tpp) REVERT: C 371 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7841 (ptpp) REVERT: C 381 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6731 (mm110) REVERT: C 386 LEU cc_start: 0.8591 (tp) cc_final: 0.8371 (tp) REVERT: C 546 ASN cc_start: 0.8134 (t0) cc_final: 0.7726 (t0) REVERT: C 554 MET cc_start: 0.7905 (tpp) cc_final: 0.7697 (tpp) REVERT: C 628 ARG cc_start: 0.7667 (mtm110) cc_final: 0.6948 (mtm180) REVERT: D 100 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7591 (tt0) REVERT: D 113 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8010 (tp30) REVERT: D 162 TYR cc_start: 0.7909 (m-10) cc_final: 0.7166 (m-10) REVERT: D 216 TYR cc_start: 0.8424 (t80) cc_final: 0.7581 (t80) REVERT: D 252 ASN cc_start: 0.8768 (t0) cc_final: 0.8253 (t0) REVERT: D 255 MET cc_start: 0.8166 (mmm) cc_final: 0.7387 (mmp) REVERT: D 381 GLN cc_start: 0.7026 (mt0) cc_final: 0.6565 (pp30) REVERT: D 406 ASP cc_start: 0.8476 (m-30) cc_final: 0.7663 (m-30) REVERT: D 580 ASP cc_start: 0.8480 (t70) cc_final: 0.8139 (t0) REVERT: D 587 GLN cc_start: 0.8642 (tt0) cc_final: 0.7996 (tm-30) REVERT: D 603 MET cc_start: 0.8118 (tmm) cc_final: 0.7909 (tmm) outliers start: 71 outliers final: 52 residues processed: 538 average time/residue: 0.1293 time to fit residues: 111.4124 Evaluate side-chains 543 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 483 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain C residue 637 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 256 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 184 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 135 GLN B 128 GLN B 129 ASN C 238 HIS ** D 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.129053 restraints weight = 32189.078| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.91 r_work: 0.3421 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21419 Z= 0.171 Angle : 0.646 8.979 29073 Z= 0.320 Chirality : 0.043 0.171 3307 Planarity : 0.004 0.056 3701 Dihedral : 4.464 52.691 2860 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.02 % Allowed : 23.63 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.17), residues: 2612 helix: 0.65 (0.14), residues: 1531 sheet: -2.78 (0.50), residues: 77 loop : -1.15 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 589 TYR 0.019 0.002 TYR D 621 PHE 0.024 0.001 PHE B 211 TRP 0.028 0.001 TRP C 29 HIS 0.004 0.001 HIS C 509 Details of bonding type rmsd covalent geometry : bond 0.00403 (21419) covalent geometry : angle 0.64562 (29073) hydrogen bonds : bond 0.03053 ( 871) hydrogen bonds : angle 3.89192 ( 2457) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 489 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7479 (tpp80) REVERT: A 35 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8319 (mmm-85) REVERT: A 46 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7609 (t0) REVERT: A 162 TYR cc_start: 0.8824 (m-10) cc_final: 0.8541 (m-10) REVERT: A 181 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7824 (mp) REVERT: A 188 ASP cc_start: 0.7444 (p0) cc_final: 0.7220 (p0) REVERT: A 252 ASN cc_start: 0.9013 (t0) cc_final: 0.8362 (t0) REVERT: A 257 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8488 (tp40) REVERT: A 296 VAL cc_start: 0.9298 (p) cc_final: 0.9060 (p) REVERT: A 314 LYS cc_start: 0.8658 (ttpp) cc_final: 0.8215 (tttp) REVERT: A 355 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5716 (tmm-80) REVERT: A 382 ASP cc_start: 0.7391 (m-30) cc_final: 0.6799 (m-30) REVERT: A 486 ILE cc_start: 0.9262 (tt) cc_final: 0.9014 (tt) REVERT: A 497 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7447 (ttp) REVERT: A 522 GLU cc_start: 0.8497 (mp0) cc_final: 0.8280 (mp0) REVERT: A 546 ASN cc_start: 0.8548 (t0) cc_final: 0.8047 (t0) REVERT: A 553 PHE cc_start: 0.6714 (t80) cc_final: 0.6007 (p90) REVERT: A 637 HIS cc_start: 0.8046 (p-80) cc_final: 0.7778 (p-80) REVERT: F 2 ASP cc_start: 0.7407 (t0) cc_final: 0.7028 (t0) REVERT: F 75 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7317 (mmmt) REVERT: F 76 MET cc_start: 0.7034 (mmm) cc_final: 0.6796 (mmm) REVERT: B 294 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7996 (tt0) REVERT: B 309 GLU cc_start: 0.8507 (mm-30) cc_final: 0.6930 (tm-30) REVERT: B 406 ASP cc_start: 0.9033 (m-30) cc_final: 0.8770 (m-30) REVERT: B 474 MET cc_start: 0.8359 (ttp) cc_final: 0.8034 (ttm) REVERT: B 485 MET cc_start: 0.8643 (ttm) cc_final: 0.8195 (mtp) REVERT: B 594 ARG cc_start: 0.8374 (mtm-85) cc_final: 0.7331 (mtm-85) REVERT: C 43 ARG cc_start: 0.8542 (mmt180) cc_final: 0.7909 (mmm-85) REVERT: C 97 LEU cc_start: 0.7481 (mm) cc_final: 0.7073 (mm) REVERT: C 126 MET cc_start: 0.8616 (mmm) cc_final: 0.8296 (mtm) REVERT: C 161 TYR cc_start: 0.9059 (t80) cc_final: 0.8608 (t80) REVERT: C 328 TYR cc_start: 0.8378 (m-10) cc_final: 0.7897 (m-10) REVERT: C 371 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7949 (ptpp) REVERT: C 381 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6738 (mm110) REVERT: C 386 LEU cc_start: 0.8625 (tp) cc_final: 0.8414 (tp) REVERT: C 546 ASN cc_start: 0.8309 (t0) cc_final: 0.7964 (t0) REVERT: C 619 CYS cc_start: 0.6055 (t) cc_final: 0.5368 (t) REVERT: C 628 ARG cc_start: 0.7734 (mtm110) cc_final: 0.6909 (mtm180) REVERT: C 630 PHE cc_start: 0.8671 (m-80) cc_final: 0.8402 (m-80) REVERT: D 100 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7654 (tt0) REVERT: D 162 TYR cc_start: 0.8047 (m-10) cc_final: 0.7215 (m-10) REVERT: D 211 PHE cc_start: 0.7873 (m-80) cc_final: 0.7523 (m-80) REVERT: D 216 TYR cc_start: 0.8476 (t80) cc_final: 0.7577 (t80) REVERT: D 255 MET cc_start: 0.8178 (mmm) cc_final: 0.7547 (mmp) REVERT: D 301 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7423 (ttmm) REVERT: D 315 GLU cc_start: 0.8305 (mp0) cc_final: 0.7797 (mm-30) REVERT: D 381 GLN cc_start: 0.7135 (mt0) cc_final: 0.6665 (pp30) REVERT: D 415 TYR cc_start: 0.8122 (t80) cc_final: 0.7640 (t80) REVERT: D 485 MET cc_start: 0.8416 (mtt) cc_final: 0.8195 (mtp) REVERT: D 556 CYS cc_start: 0.8522 (m) cc_final: 0.8174 (t) REVERT: D 580 ASP cc_start: 0.8559 (t70) cc_final: 0.8228 (t0) REVERT: D 587 GLN cc_start: 0.8709 (tt0) cc_final: 0.8062 (tm-30) outliers start: 68 outliers final: 51 residues processed: 526 average time/residue: 0.1305 time to fit residues: 109.6685 Evaluate side-chains 529 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 473 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain E residue 704 ILE Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 342 CYS Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 525 ASP Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 91 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 146 optimal weight: 0.0970 chunk 190 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 128 GLN B 129 ASN D 267 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.157820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132264 restraints weight = 32299.845| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.02 r_work: 0.3451 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21419 Z= 0.115 Angle : 0.622 11.204 29073 Z= 0.304 Chirality : 0.041 0.168 3307 Planarity : 0.003 0.056 3701 Dihedral : 4.403 53.759 2860 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.27 % Allowed : 24.92 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.17), residues: 2612 helix: 0.79 (0.14), residues: 1523 sheet: -2.79 (0.50), residues: 77 loop : -1.09 (0.21), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 414 TYR 0.016 0.001 TYR A 415 PHE 0.025 0.001 PHE B 211 TRP 0.023 0.001 TRP C 29 HIS 0.003 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00267 (21419) covalent geometry : angle 0.62236 (29073) hydrogen bonds : bond 0.02790 ( 871) hydrogen bonds : angle 3.75798 ( 2457) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5224 Ramachandran restraints generated. 2612 Oldfield, 0 Emsley, 2612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 493 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7697 (mmm-85) cc_final: 0.7477 (tpp80) REVERT: A 35 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8309 (mmm-85) REVERT: A 46 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7607 (t0) REVERT: A 162 TYR cc_start: 0.8661 (m-10) cc_final: 0.8112 (m-10) REVERT: A 181 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7939 (mp) REVERT: A 188 ASP cc_start: 0.7466 (p0) cc_final: 0.7248 (p0) REVERT: A 252 ASN cc_start: 0.8968 (t0) cc_final: 0.8305 (t0) REVERT: A 257 GLN cc_start: 0.8746 (tp-100) cc_final: 0.8451 (tp40) REVERT: A 288 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: A 296 VAL cc_start: 0.9289 (p) cc_final: 0.9043 (p) REVERT: A 314 LYS cc_start: 0.8649 (ttpp) cc_final: 0.8188 (tttp) REVERT: A 382 ASP cc_start: 0.7416 (m-30) cc_final: 0.6835 (m-30) REVERT: A 442 MET cc_start: 0.8471 (mmt) cc_final: 0.8130 (mmt) REVERT: A 486 ILE cc_start: 0.9168 (tt) cc_final: 0.8915 (tt) REVERT: A 497 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7441 (ttp) REVERT: A 522 GLU cc_start: 0.8514 (mp0) cc_final: 0.8297 (mp0) REVERT: A 525 ASP cc_start: 0.7594 (t0) cc_final: 0.7388 (t0) REVERT: A 546 ASN cc_start: 0.8506 (t0) cc_final: 0.8007 (t0) REVERT: A 553 PHE cc_start: 0.6667 (t80) cc_final: 0.5909 (p90) REVERT: A 570 MET cc_start: 0.9065 (tpp) cc_final: 0.8132 (mmt) REVERT: A 592 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8869 (mp) REVERT: A 637 HIS cc_start: 0.8008 (p-80) cc_final: 0.7780 (p-80) REVERT: F 2 ASP cc_start: 0.7366 (t0) cc_final: 0.6983 (t0) REVERT: F 75 LYS cc_start: 0.7485 (mmtt) cc_final: 0.6945 (mmtm) REVERT: F 76 MET cc_start: 0.7048 (mmm) cc_final: 0.6798 (mmm) REVERT: B 99 MET cc_start: 0.8075 (mtm) cc_final: 0.7755 (mtm) REVERT: B 262 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8305 (tmtt) REVERT: B 294 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7898 (tt0) REVERT: B 309 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7143 (tt0) REVERT: B 406 ASP cc_start: 0.9009 (m-30) cc_final: 0.8748 (m-30) REVERT: B 474 MET cc_start: 0.8407 (ttp) cc_final: 0.8181 (ttm) REVERT: C 43 ARG cc_start: 0.8534 (mmt180) cc_final: 0.7904 (mmm-85) REVERT: C 97 LEU cc_start: 0.7473 (mm) cc_final: 0.7076 (mm) REVERT: C 126 MET cc_start: 0.8539 (mmm) cc_final: 0.8176 (mtp) REVERT: C 161 TYR cc_start: 0.8941 (t80) cc_final: 0.8679 (t80) REVERT: C 328 TYR cc_start: 0.8241 (m-10) cc_final: 0.7866 (m-10) REVERT: C 340 MET cc_start: 0.9042 (mmm) cc_final: 0.7948 (tpp) REVERT: C 371 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7808 (ptpp) REVERT: C 381 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6710 (mm110) REVERT: C 447 MET cc_start: 0.6777 (mmt) cc_final: 0.6524 (mmt) REVERT: C 546 ASN cc_start: 0.8214 (t0) cc_final: 0.7809 (t0) REVERT: C 619 CYS cc_start: 0.5981 (t) cc_final: 0.5260 (t) REVERT: C 628 ARG cc_start: 0.7696 (mtm110) cc_final: 0.6902 (mtm180) REVERT: D 100 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7586 (tt0) REVERT: D 162 TYR cc_start: 0.7872 (m-10) cc_final: 0.7103 (m-10) REVERT: D 211 PHE cc_start: 0.7760 (m-80) cc_final: 0.7459 (m-80) REVERT: D 216 TYR cc_start: 0.8440 (t80) cc_final: 0.7584 (t80) REVERT: D 252 ASN cc_start: 0.8729 (t0) cc_final: 0.8317 (t0) REVERT: D 255 MET cc_start: 0.8161 (mmm) cc_final: 0.7425 (mmp) REVERT: D 301 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7393 (ttmm) REVERT: D 315 GLU cc_start: 0.8183 (mp0) cc_final: 0.7761 (mm-30) REVERT: D 381 GLN cc_start: 0.7051 (mt0) cc_final: 0.6598 (pp30) REVERT: D 415 TYR cc_start: 0.8035 (t80) cc_final: 0.7554 (t80) REVERT: D 442 MET cc_start: 0.7500 (mmt) cc_final: 0.7282 (tpp) REVERT: D 485 MET cc_start: 0.8462 (mtt) cc_final: 0.8224 (mtp) REVERT: D 556 CYS cc_start: 0.8529 (m) cc_final: 0.8137 (t) REVERT: D 580 ASP cc_start: 0.8504 (t70) cc_final: 0.8150 (t0) REVERT: D 587 GLN cc_start: 0.8694 (tt0) cc_final: 0.8089 (tm-30) REVERT: D 603 MET cc_start: 0.8375 (tmm) cc_final: 0.8151 (tmm) outliers start: 51 outliers final: 42 residues processed: 521 average time/residue: 0.1319 time to fit residues: 109.6235 Evaluate side-chains 530 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 482 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 497 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 74 ARG Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 CYS Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 371 LYS Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 398 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 592 LEU Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 537 PHE Chi-restraints excluded: chain D residue 592 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 162 optimal weight: 0.2980 chunk 106 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 220 optimal weight: 0.0970 chunk 192 optimal weight: 0.8980 chunk 121 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 98 optimal weight: 0.6980 chunk 114 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN B 129 ASN C 158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134784 restraints weight = 32138.749| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.93 r_work: 0.3478 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21419 Z= 0.108 Angle : 0.612 11.622 29073 Z= 0.299 Chirality : 0.041 0.177 3307 Planarity : 0.003 0.054 3701 Dihedral : 4.316 54.243 2860 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.27 % Allowed : 25.10 % Favored : 72.63 % 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: 0.05 (0.17), residues: 2612 helix: 0.88 (0.14), residues: 1533 sheet: -2.71 (0.51), residues: 77 loop : -1.01 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 414 TYR 0.017 0.001 TYR A 415 PHE 0.029 0.001 PHE A 534 TRP 0.026 0.001 TRP D 629 HIS 0.002 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00244 (21419) covalent geometry : angle 0.61224 (29073) hydrogen bonds : bond 0.02693 ( 871) hydrogen bonds : angle 3.66943 ( 2457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4454.99 seconds wall clock time: 77 minutes 15.98 seconds (4635.98 seconds total)