Starting phenix.real_space_refine on Sat Jul 4 13:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12ag_76261/07_2026/12ag_76261.cif Found real_map, /net/cci-nas-00/data/ceres_data/12ag_76261/07_2026/12ag_76261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/12ag_76261/07_2026/12ag_76261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12ag_76261/07_2026/12ag_76261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/12ag_76261/07_2026/12ag_76261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12ag_76261/07_2026/12ag_76261.map" } resolution = 3.48 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= 0.003 sd= 0.020 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 P 12 5.49 5 S 160 5.16 5 C 13594 2.51 5 N 3332 2.21 5 O 3596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20694 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "B" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "D" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4895 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 26, 'TRANS': 583} Chain: "A" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 274 Unusual residues: {'PCW': 1, 'POV': 3, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 288 Unusual residues: {'PCW': 1, 'POV': 3, 'SPM': 1, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 274 Unusual residues: {'PCW': 1, 'POV': 3, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 274 Unusual residues: {'PCW': 1, 'POV': 3, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.44, per 1000 atoms: 0.21 Number of scatterers: 20694 At special positions: 0 Unit cell: (124.504, 125.292, 120.564, 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) S 160 16.00 P 12 15.00 O 3596 8.00 N 3332 7.00 C 13594 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: 1.64 Conformation dependent library (CDL) restraints added in 906.2 milliseconds 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4608 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 67.3% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.677A pdb=" N ASP A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN A 41 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.612A pdb=" N LEU A 88 " --> pdb=" O HIS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.550A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.761A pdb=" N GLU A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.608A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 206 removed outlier: 3.557A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 222 removed outlier: 3.572A pdb=" N ALA A 212 " --> pdb=" O ASN A 208 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.611A 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 291 through 299 removed outlier: 3.704A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.767A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 325 through 349 removed outlier: 3.765A pdb=" N LEU A 332 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.754A pdb=" N ARG A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 416 No H-bonds generated for 'chain 'A' and resid 414 through 416' Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.989A pdb=" N LEU A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.656A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 489 through 512 removed outlier: 6.260A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.531A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.851A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE A 564 " --> pdb=" O ALA A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.602A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 607 removed outlier: 3.534A pdb=" N ALA A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 29 through 47 removed outlier: 3.676A pdb=" N ASP B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.611A pdb=" N LEU B 88 " --> pdb=" O HIS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.550A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.760A pdb=" N GLU B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.609A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 Processing helix chain 'B' and resid 149 through 153 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 206 removed outlier: 3.557A pdb=" N ILE B 202 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.572A pdb=" N ALA B 212 " --> pdb=" O ASN B 208 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.611A 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 291 through 299 removed outlier: 3.704A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.766A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 324 Processing helix chain 'B' and resid 325 through 349 removed outlier: 3.764A pdb=" N LEU B 332 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.755A pdb=" N ARG B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.988A pdb=" N LEU B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.656A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 488 Processing helix chain 'B' and resid 489 through 512 removed outlier: 6.260A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 515 No H-bonds generated for 'chain 'B' and resid 513 through 515' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.531A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.852A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 564 " --> pdb=" O ALA B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.602A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 607 removed outlier: 3.534A pdb=" N ALA B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 29 through 47 removed outlier: 3.677A pdb=" N ASP C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN C 41 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.612A pdb=" N LEU C 88 " --> pdb=" O HIS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.549A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.760A pdb=" N GLU C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.608A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 165 through 173 Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 206 removed outlier: 3.556A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 222 removed outlier: 3.571A pdb=" N ALA C 212 " --> pdb=" O ASN C 208 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 251 removed outlier: 3.612A 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 291 through 299 removed outlier: 3.703A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.766A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 324 Processing helix chain 'C' and resid 325 through 349 removed outlier: 3.764A pdb=" N LEU C 332 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.755A pdb=" N ARG C 409 " --> pdb=" O PRO C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 416 No H-bonds generated for 'chain 'C' and resid 414 through 416' Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.987A pdb=" N LEU C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.656A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 Processing helix chain 'C' and resid 477 through 488 Processing helix chain 'C' and resid 489 through 512 removed outlier: 6.259A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.531A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.852A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 564 " --> pdb=" O ALA C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.602A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 607 removed outlier: 3.534A pdb=" N ALA C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 29 through 47 removed outlier: 3.676A pdb=" N ASP D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 41 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 removed outlier: 3.612A pdb=" N LEU D 88 " --> pdb=" O HIS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.550A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.761A pdb=" N GLU D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.609A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 206 removed outlier: 3.556A pdb=" N ILE D 202 " --> pdb=" O THR D 198 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 222 removed outlier: 3.573A pdb=" N ALA D 212 " --> pdb=" O ASN D 208 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.612A 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 291 through 299 removed outlier: 3.703A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.766A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 Processing helix chain 'D' and resid 325 through 349 removed outlier: 3.765A pdb=" N LEU D 332 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS D 342 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.754A pdb=" N ARG D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 removed outlier: 3.988A pdb=" N LEU D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.656A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN D 464 " --> pdb=" O LEU D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 476 Processing helix chain 'D' and resid 477 through 488 Processing helix chain 'D' and resid 489 through 512 removed outlier: 6.259A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 511 " --> pdb=" O ALA D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 515 No H-bonds generated for 'chain 'D' and resid 513 through 515' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.530A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.851A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE D 564 " --> pdb=" O ALA D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.602A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 607 removed outlier: 3.533A pdb=" N ALA D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 276 through 278 Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 276 through 278 Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 276 through 278 Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1013 hydrogen bonds defined for protein. 2859 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: 3.26 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.29: 3212 1.29 - 1.45: 5594 1.45 - 1.60: 11970 1.60 - 1.75: 89 1.75 - 1.91: 296 Bond restraints: 21161 Sorted by residual: bond pdb=" CAV Y01 B 701 " pdb=" CAZ Y01 B 701 " ideal model delta sigma weight residual 1.507 1.905 -0.398 2.00e-02 2.50e+03 3.97e+02 bond pdb=" CAV Y01 D 704 " pdb=" CAZ Y01 D 704 " ideal model delta sigma weight residual 1.507 1.905 -0.398 2.00e-02 2.50e+03 3.96e+02 bond pdb=" CAV Y01 B 703 " pdb=" CAZ Y01 B 703 " ideal model delta sigma weight residual 1.507 1.905 -0.398 2.00e-02 2.50e+03 3.95e+02 bond pdb=" CAV Y01 A 801 " pdb=" CAZ Y01 A 801 " ideal model delta sigma weight residual 1.507 1.904 -0.397 2.00e-02 2.50e+03 3.94e+02 bond pdb=" CAV Y01 C 704 " pdb=" CAZ Y01 C 704 " ideal model delta sigma weight residual 1.507 1.903 -0.396 2.00e-02 2.50e+03 3.93e+02 ... (remaining 21156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 26969 2.86 - 5.71: 1191 5.71 - 8.57: 338 8.57 - 11.42: 86 11.42 - 14.28: 44 Bond angle restraints: 28628 Sorted by residual: angle pdb=" N ALA C 469 " pdb=" CA ALA C 469 " pdb=" C ALA C 469 " ideal model delta sigma weight residual 114.56 107.89 6.67 1.27e+00 6.20e-01 2.75e+01 angle pdb=" N ALA B 469 " pdb=" CA ALA B 469 " pdb=" C ALA B 469 " ideal model delta sigma weight residual 114.56 107.91 6.65 1.27e+00 6.20e-01 2.74e+01 angle pdb=" N ALA D 469 " pdb=" CA ALA D 469 " pdb=" C ALA D 469 " ideal model delta sigma weight residual 114.56 107.92 6.64 1.27e+00 6.20e-01 2.73e+01 angle pdb=" N ALA A 469 " pdb=" CA ALA A 469 " pdb=" C ALA A 469 " ideal model delta sigma weight residual 114.56 107.93 6.63 1.27e+00 6.20e-01 2.73e+01 angle pdb=" C GLY C 226 " pdb=" N ASP C 227 " pdb=" CA ASP C 227 " ideal model delta sigma weight residual 121.54 131.18 -9.64 1.91e+00 2.74e-01 2.55e+01 ... (remaining 28623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 12369 27.92 - 55.85: 715 55.85 - 83.77: 202 83.77 - 111.69: 81 111.69 - 139.61: 36 Dihedral angle restraints: 13403 sinusoidal: 6267 harmonic: 7136 Sorted by residual: dihedral pdb=" CA ASP D 227 " pdb=" C ASP D 227 " pdb=" N HIS D 228 " pdb=" CA HIS D 228 " ideal model delta harmonic sigma weight residual -180.00 -136.17 -43.83 0 5.00e+00 4.00e-02 7.68e+01 dihedral pdb=" CA ASP A 227 " pdb=" C ASP A 227 " pdb=" N HIS A 228 " pdb=" CA HIS A 228 " ideal model delta harmonic sigma weight residual -180.00 -136.18 -43.82 0 5.00e+00 4.00e-02 7.68e+01 dihedral pdb=" CA ASP B 227 " pdb=" C ASP B 227 " pdb=" N HIS B 228 " pdb=" CA HIS B 228 " ideal model delta harmonic sigma weight residual -180.00 -136.18 -43.82 0 5.00e+00 4.00e-02 7.68e+01 ... (remaining 13400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.983: 3148 0.983 - 1.967: 0 1.967 - 2.950: 0 2.950 - 3.933: 1 3.933 - 4.916: 47 Chirality restraints: 3196 Sorted by residual: chirality pdb=" CBC Y01 B 703 " pdb=" CAR Y01 B 703 " pdb=" CAV Y01 B 703 " pdb=" OAW Y01 B 703 " both_signs ideal model delta sigma weight residual False -2.54 2.37 -4.92 2.00e-01 2.50e+01 6.04e+02 chirality pdb=" CBC Y01 D 704 " pdb=" CAR Y01 D 704 " pdb=" CAV Y01 D 704 " pdb=" OAW Y01 D 704 " both_signs ideal model delta sigma weight residual False -2.54 2.37 -4.91 2.00e-01 2.50e+01 6.03e+02 chirality pdb=" CBC Y01 A 801 " pdb=" CAR Y01 A 801 " pdb=" CAV Y01 A 801 " pdb=" OAW Y01 A 801 " both_signs ideal model delta sigma weight residual False -2.54 2.36 -4.90 2.00e-01 2.50e+01 6.01e+02 ... (remaining 3193 not shown) Planarity restraints: 3500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 476 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO D 477 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 477 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 477 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 476 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO A 477 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO A 477 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 477 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " 0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO B 477 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " 0.042 5.00e-02 4.00e+02 ... (remaining 3497 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4958 2.79 - 3.32: 19715 3.32 - 3.84: 33962 3.84 - 4.37: 41018 4.37 - 4.90: 67946 Nonbonded interactions: 167599 Sorted by model distance: nonbonded pdb=" OH TYR A 377 " pdb=" OE1 GLU A 389 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR D 377 " pdb=" OE1 GLU D 389 " model vdw 2.259 3.040 nonbonded pdb=" OH TYR B 377 " pdb=" OE1 GLU B 389 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR C 377 " pdb=" OE1 GLU C 389 " model vdw 2.260 3.040 nonbonded pdb=" O ILE A 283 " pdb=" OG SER A 291 " model vdw 2.280 3.040 ... (remaining 167594 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 28 through 637 or resid 807)) selection = (chain 'B' and (resid 28 through 637 or resid 707)) selection = (chain 'C' and (resid 28 through 637 or resid 707)) selection = (chain 'D' and (resid 28 through 637 or resid 707)) } 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=0.45 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 18.380 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.023 0.398 21161 Z= 1.152 Angle : 1.588 14.276 28628 Z= 0.788 Chirality : 0.535 4.916 3196 Planarity : 0.008 0.075 3500 Dihedral : 21.501 139.613 8795 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 8.22 % Favored : 91.28 % Rotamer: Outliers : 1.51 % Allowed : 3.83 % Favored : 94.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -4.84 (0.13), residues: 2432 helix: -3.16 (0.09), residues: 1472 sheet: -5.24 (0.22), residues: 76 loop : -2.76 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 470 TYR 0.015 0.002 TYR D 524 PHE 0.025 0.003 PHE B 169 TRP 0.022 0.003 TRP C 629 HIS 0.009 0.002 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.02330 / 1.15 (21161) covalent geometry : angle 1.58761 / 0.79 (28628) hydrogen bonds : bond 0.29569 / 19.98 ( 1013) hydrogen bonds : angle 8.94862 / 6.31 ( 2859) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 643 time to evaluate : 0.779 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: symmetry clash 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 40 GLN cc_start: 0.9285 (tt0) cc_final: 0.9046 (tt0) REVERT: A 96 MET cc_start: 0.9032 (mmt) cc_final: 0.8618 (mmm) REVERT: A 107 PHE cc_start: 0.8220 (m-10) cc_final: 0.7841 (m-80) REVERT: A 121 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9071 (tm) REVERT: A 123 ILE cc_start: 0.9716 (mt) cc_final: 0.9396 (tt) REVERT: A 295 LEU cc_start: 0.9213 (mt) cc_final: 0.8954 (mt) REVERT: A 298 THR cc_start: 0.8841 (m) cc_final: 0.8543 (p) REVERT: A 300 LYS cc_start: 0.8863 (mppt) cc_final: 0.8432 (mmtt) REVERT: A 310 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8099 (mm110) REVERT: A 322 LYS cc_start: 0.9321 (mtpm) cc_final: 0.9048 (mmtt) REVERT: A 328 TYR cc_start: 0.8761 (m-10) cc_final: 0.8550 (m-80) REVERT: A 358 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8380 (t0) REVERT: A 365 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7916 (t0) REVERT: A 435 MET cc_start: 0.9395 (mmt) cc_final: 0.8670 (mmm) REVERT: A 473 GLN cc_start: 0.8522 (tt0) cc_final: 0.7145 (tt0) REVERT: A 481 MET cc_start: 0.9167 (mtt) cc_final: 0.8940 (mtp) REVERT: A 569 LEU cc_start: 0.9131 (tt) cc_final: 0.8791 (tt) REVERT: A 583 TRP cc_start: 0.8494 (t60) cc_final: 0.8113 (t60) REVERT: A 593 TRP cc_start: 0.9241 (t60) cc_final: 0.8636 (t60) REVERT: B 40 GLN cc_start: 0.9327 (tt0) cc_final: 0.8912 (tt0) REVERT: B 78 MET cc_start: 0.8066 (mpt) cc_final: 0.7157 (mpt) REVERT: B 96 MET cc_start: 0.9052 (mmt) cc_final: 0.8689 (mmm) REVERT: B 107 PHE cc_start: 0.8218 (m-10) cc_final: 0.7811 (m-10) REVERT: B 123 ILE cc_start: 0.9744 (mt) cc_final: 0.9393 (tt) REVERT: B 130 MET cc_start: 0.7621 (tpt) cc_final: 0.7315 (tpt) REVERT: B 295 LEU cc_start: 0.9143 (mt) cc_final: 0.8867 (mt) REVERT: B 298 THR cc_start: 0.8845 (m) cc_final: 0.8555 (p) REVERT: B 300 LYS cc_start: 0.8989 (mppt) cc_final: 0.8545 (mmtt) REVERT: B 310 GLN cc_start: 0.8364 (mm-40) cc_final: 0.8126 (mm110) REVERT: B 322 LYS cc_start: 0.9329 (mtpm) cc_final: 0.9031 (mmtt) REVERT: B 328 TYR cc_start: 0.8799 (m-10) cc_final: 0.8563 (m-80) REVERT: B 359 ARG cc_start: 0.7587 (ttp80) cc_final: 0.7308 (ttp80) REVERT: B 365 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.8139 (t0) REVERT: B 403 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8062 (tt0) REVERT: B 426 HIS cc_start: 0.8704 (m90) cc_final: 0.8384 (m-70) REVERT: B 435 MET cc_start: 0.9268 (mmt) cc_final: 0.8565 (mmm) REVERT: B 481 MET cc_start: 0.9211 (mtt) cc_final: 0.8992 (mtp) REVERT: B 569 LEU cc_start: 0.9183 (tt) cc_final: 0.8839 (tt) REVERT: B 578 MET cc_start: 0.8963 (mtm) cc_final: 0.8757 (mtp) REVERT: B 583 TRP cc_start: 0.8532 (t60) cc_final: 0.8094 (t60) REVERT: B 593 TRP cc_start: 0.9277 (t60) cc_final: 0.8636 (t60) REVERT: C 40 GLN cc_start: 0.9323 (tt0) cc_final: 0.9119 (tt0) REVERT: C 96 MET cc_start: 0.9101 (mmt) cc_final: 0.8636 (mmm) REVERT: C 121 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9062 (tm) REVERT: C 123 ILE cc_start: 0.9742 (mt) cc_final: 0.9369 (tt) REVERT: C 298 THR cc_start: 0.8938 (m) cc_final: 0.8629 (p) REVERT: C 300 LYS cc_start: 0.8990 (mppt) cc_final: 0.8487 (mmpt) REVERT: C 315 GLU cc_start: 0.8839 (mp0) cc_final: 0.8342 (mp0) REVERT: C 322 LYS cc_start: 0.9226 (mtpm) cc_final: 0.8941 (mmtt) REVERT: C 365 ASN cc_start: 0.8391 (OUTLIER) cc_final: 0.8081 (t0) REVERT: C 481 MET cc_start: 0.9304 (mtt) cc_final: 0.9048 (mtp) REVERT: C 569 LEU cc_start: 0.9207 (tt) cc_final: 0.8981 (tt) REVERT: C 583 TRP cc_start: 0.8558 (t60) cc_final: 0.8023 (t60) REVERT: C 593 TRP cc_start: 0.9456 (t60) cc_final: 0.8759 (t60) REVERT: D 40 GLN cc_start: 0.9282 (tt0) cc_final: 0.9075 (tt0) REVERT: D 96 MET cc_start: 0.9038 (mmt) cc_final: 0.8532 (mmm) REVERT: D 99 MET cc_start: 0.8815 (ptt) cc_final: 0.8344 (ptm) REVERT: D 107 PHE cc_start: 0.8222 (m-10) cc_final: 0.7897 (m-80) REVERT: D 123 ILE cc_start: 0.9700 (mt) cc_final: 0.9376 (tt) REVERT: D 298 THR cc_start: 0.8881 (m) cc_final: 0.8574 (p) REVERT: D 300 LYS cc_start: 0.8832 (mppt) cc_final: 0.8359 (mmtt) REVERT: D 310 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8103 (mm110) REVERT: D 322 LYS cc_start: 0.9296 (mtpm) cc_final: 0.9049 (mmtt) REVERT: D 358 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8463 (t0) REVERT: D 365 ASN cc_start: 0.8281 (OUTLIER) cc_final: 0.7969 (t0) REVERT: D 473 GLN cc_start: 0.8559 (tt0) cc_final: 0.6841 (tt0) REVERT: D 583 TRP cc_start: 0.8494 (t60) cc_final: 0.8017 (t60) REVERT: D 593 TRP cc_start: 0.9322 (t60) cc_final: 0.8595 (t60) outliers start: 32 outliers final: 4 residues processed: 671 average time/residue: 0.1504 time to fit residues: 153.5635 Evaluate side-chains 431 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 419 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 365 ASN Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain D residue 358 ASN Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 73 HIS ** A 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 HIS A 174 ASN A 214 GLN A 228 HIS A 238 HIS A 267 GLN A 358 ASN A 370 GLN A 522 HIS A 596 GLN B 73 HIS ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 HIS B 238 HIS B 267 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 426 HIS B 522 HIS B 596 GLN C 73 HIS ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS C 174 ASN C 214 GLN C 238 HIS C 267 GLN ** C 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 522 HIS C 596 GLN D 73 HIS D 118 GLN D 165 HIS D 174 ASN D 214 GLN D 228 HIS D 238 HIS D 267 GLN D 358 ASN ** D 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 426 HIS D 522 HIS D 596 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.105772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079516 restraints weight = 48272.703| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.50 r_work: 0.2949 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21161 Z= 0.227 Angle : 0.810 9.432 28628 Z= 0.411 Chirality : 0.045 0.246 3196 Planarity : 0.006 0.054 3500 Dihedral : 17.341 141.255 4111 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.02 % Favored : 91.65 % Rotamer: Outliers : 3.31 % Allowed : 12.67 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % 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: -2.00 (0.16), residues: 2432 helix: -0.48 (0.12), residues: 1448 sheet: -5.42 (0.19), residues: 76 loop : -2.25 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 75 TYR 0.020 0.002 TYR B 270 PHE 0.031 0.002 PHE B 434 TRP 0.016 0.002 TRP D 268 HIS 0.008 0.001 HIS C 426 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (21161) covalent geometry : angle 0.80956 / 0.41 (28628) hydrogen bonds : bond 0.05413 / 3.66 ( 1013) hydrogen bonds : angle 5.00606 / 3.53 ( 2859) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 453 time to evaluate : 0.614 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: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9059 (mmt) cc_final: 0.8748 (mmm) REVERT: A 99 MET cc_start: 0.8682 (ptt) cc_final: 0.8358 (ptm) REVERT: A 300 LYS cc_start: 0.8836 (mppt) cc_final: 0.8456 (mmtt) REVERT: A 315 GLU cc_start: 0.9213 (mp0) cc_final: 0.8641 (mp0) REVERT: A 322 LYS cc_start: 0.9443 (mtpm) cc_final: 0.9108 (mmtt) REVERT: A 365 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7870 (t0) REVERT: A 435 MET cc_start: 0.9506 (mmt) cc_final: 0.8868 (mmm) REVERT: A 583 TRP cc_start: 0.8949 (t60) cc_final: 0.8455 (t60) REVERT: A 593 TRP cc_start: 0.9474 (t60) cc_final: 0.8591 (t60) REVERT: B 96 MET cc_start: 0.9110 (mmt) cc_final: 0.8746 (mmm) REVERT: B 99 MET cc_start: 0.8669 (ptt) cc_final: 0.8316 (ptm) REVERT: B 215 MET cc_start: 0.9173 (mmp) cc_final: 0.8878 (tpp) REVERT: B 300 LYS cc_start: 0.9000 (mppt) cc_final: 0.8583 (mmtt) REVERT: B 328 TYR cc_start: 0.9109 (m-10) cc_final: 0.8735 (m-80) REVERT: B 583 TRP cc_start: 0.8905 (t60) cc_final: 0.8412 (t60) REVERT: B 593 TRP cc_start: 0.9500 (t60) cc_final: 0.8704 (t60) REVERT: C 96 MET cc_start: 0.9160 (mmt) cc_final: 0.8729 (mmm) REVERT: C 99 MET cc_start: 0.8632 (ptt) cc_final: 0.8368 (ptm) REVERT: C 110 MET cc_start: 0.8424 (mtt) cc_final: 0.8216 (mtm) REVERT: C 295 LEU cc_start: 0.9237 (mt) cc_final: 0.9033 (mt) REVERT: C 298 THR cc_start: 0.9063 (m) cc_final: 0.8773 (p) REVERT: C 300 LYS cc_start: 0.9180 (mppt) cc_final: 0.8233 (mmtt) REVERT: C 315 GLU cc_start: 0.9132 (mp0) cc_final: 0.8673 (mp0) REVERT: C 322 LYS cc_start: 0.9424 (mtpm) cc_final: 0.9092 (mmtt) REVERT: C 418 GLN cc_start: 0.8823 (mp10) cc_final: 0.8583 (mp10) REVERT: C 435 MET cc_start: 0.9428 (mmm) cc_final: 0.8498 (mmm) REVERT: C 481 MET cc_start: 0.9345 (mtt) cc_final: 0.9092 (mtp) REVERT: C 491 MET cc_start: 0.8392 (tmm) cc_final: 0.8017 (tpt) REVERT: C 569 LEU cc_start: 0.9166 (tt) cc_final: 0.8947 (tt) REVERT: C 583 TRP cc_start: 0.8896 (t60) cc_final: 0.8380 (t60) REVERT: C 593 TRP cc_start: 0.9536 (t60) cc_final: 0.8712 (t60) REVERT: D 96 MET cc_start: 0.9107 (mmt) cc_final: 0.8746 (mmm) REVERT: D 99 MET cc_start: 0.8672 (ptt) cc_final: 0.8461 (ptm) REVERT: D 203 LEU cc_start: 0.9451 (mt) cc_final: 0.9216 (mt) REVERT: D 294 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8721 (mt-10) REVERT: D 295 LEU cc_start: 0.9242 (mt) cc_final: 0.9036 (mt) REVERT: D 298 THR cc_start: 0.9055 (m) cc_final: 0.8760 (p) REVERT: D 300 LYS cc_start: 0.8805 (mppt) cc_final: 0.8229 (mmtt) REVERT: D 315 GLU cc_start: 0.9196 (mp0) cc_final: 0.8622 (mp0) REVERT: D 322 LYS cc_start: 0.9440 (mtpm) cc_final: 0.9119 (mmtt) REVERT: D 359 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7300 (ttp80) REVERT: D 365 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.8009 (t0) REVERT: D 435 MET cc_start: 0.9420 (mmm) cc_final: 0.8498 (mmm) REVERT: D 553 PHE cc_start: 0.8866 (t80) cc_final: 0.8428 (t80) REVERT: D 583 TRP cc_start: 0.8908 (t60) cc_final: 0.8412 (t60) REVERT: D 593 TRP cc_start: 0.9485 (t60) cc_final: 0.8605 (t60) outliers start: 70 outliers final: 25 residues processed: 489 average time/residue: 0.1242 time to fit residues: 97.7612 Evaluate side-chains 413 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 386 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 228 HIS Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 365 ASN Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 241 optimal weight: 10.0000 chunk 28 optimal weight: 0.5980 chunk 127 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 201 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 174 ASN C 118 GLN C 310 GLN D 36 GLN ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.107541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.082134 restraints weight = 48129.372| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.43 r_work: 0.3043 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21161 Z= 0.157 Angle : 0.719 7.808 28628 Z= 0.362 Chirality : 0.042 0.251 3196 Planarity : 0.005 0.050 3500 Dihedral : 16.416 138.088 4099 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.52 % Favored : 92.19 % Rotamer: Outliers : 3.02 % Allowed : 15.64 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.17), residues: 2432 helix: 0.36 (0.13), residues: 1452 sheet: -5.23 (0.21), residues: 68 loop : -1.98 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 305 TYR 0.021 0.002 TYR A 270 PHE 0.030 0.001 PHE D 434 TRP 0.012 0.001 TRP D 268 HIS 0.015 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (21161) covalent geometry : angle 0.71888 / 0.36 (28628) hydrogen bonds : bond 0.04424 / 2.98 ( 1013) hydrogen bonds : angle 4.62613 / 3.30 ( 2859) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 439 time to evaluate : 0.751 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: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.9052 (mmt) cc_final: 0.8782 (mmm) REVERT: A 99 MET cc_start: 0.8634 (ptt) cc_final: 0.8316 (ptm) REVERT: A 300 LYS cc_start: 0.8789 (mppt) cc_final: 0.8448 (mmtt) REVERT: A 315 GLU cc_start: 0.9179 (mp0) cc_final: 0.8691 (mp0) REVERT: A 322 LYS cc_start: 0.9460 (mtpm) cc_final: 0.9154 (mmtt) REVERT: A 365 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7856 (t0) REVERT: A 553 PHE cc_start: 0.8877 (t80) cc_final: 0.8553 (t80) REVERT: A 583 TRP cc_start: 0.8982 (t60) cc_final: 0.8494 (t60) REVERT: A 593 TRP cc_start: 0.9453 (t60) cc_final: 0.8563 (t60) REVERT: B 78 MET cc_start: 0.8562 (mpp) cc_final: 0.8345 (mpp) REVERT: B 96 MET cc_start: 0.9059 (mmt) cc_final: 0.8746 (mmm) REVERT: B 99 MET cc_start: 0.8605 (ptt) cc_final: 0.8393 (ptm) REVERT: B 113 GLU cc_start: 0.8993 (pp20) cc_final: 0.8629 (pp20) REVERT: B 215 MET cc_start: 0.9125 (mmp) cc_final: 0.8826 (tpp) REVERT: B 249 VAL cc_start: 0.9437 (t) cc_final: 0.9188 (m) REVERT: B 300 LYS cc_start: 0.8884 (mppt) cc_final: 0.8566 (mmtt) REVERT: B 302 ARG cc_start: 0.8385 (mmm160) cc_final: 0.8032 (mmm160) REVERT: B 315 GLU cc_start: 0.9170 (mp0) cc_final: 0.8683 (mp0) REVERT: B 328 TYR cc_start: 0.9091 (m-10) cc_final: 0.8818 (m-80) REVERT: B 435 MET cc_start: 0.9279 (mmm) cc_final: 0.8451 (mmm) REVERT: B 583 TRP cc_start: 0.8974 (t60) cc_final: 0.8497 (t60) REVERT: B 593 TRP cc_start: 0.9464 (t60) cc_final: 0.8604 (t60) REVERT: B 603 MET cc_start: 0.9045 (tmm) cc_final: 0.8832 (tmm) REVERT: B 607 LYS cc_start: 0.9272 (mtmt) cc_final: 0.9054 (mtmm) REVERT: C 96 MET cc_start: 0.9129 (mmt) cc_final: 0.8698 (mmm) REVERT: C 99 MET cc_start: 0.8661 (ptt) cc_final: 0.8327 (ptm) REVERT: C 113 GLU cc_start: 0.8933 (pp20) cc_final: 0.8553 (pp20) REVERT: C 298 THR cc_start: 0.9053 (m) cc_final: 0.8833 (t) REVERT: C 300 LYS cc_start: 0.9035 (mppt) cc_final: 0.8580 (mmtt) REVERT: C 315 GLU cc_start: 0.9089 (mp0) cc_final: 0.8618 (mp0) REVERT: C 322 LYS cc_start: 0.9446 (mtpm) cc_final: 0.9139 (mmtt) REVERT: C 435 MET cc_start: 0.9322 (mmm) cc_final: 0.8391 (mmm) REVERT: C 483 GLN cc_start: 0.9066 (OUTLIER) cc_final: 0.8799 (tt0) REVERT: C 491 MET cc_start: 0.8316 (tmm) cc_final: 0.7912 (tpt) REVERT: C 583 TRP cc_start: 0.8961 (t60) cc_final: 0.8434 (t60) REVERT: C 593 TRP cc_start: 0.9479 (t60) cc_final: 0.8715 (t60) REVERT: D 40 GLN cc_start: 0.9435 (tt0) cc_final: 0.9029 (tm-30) REVERT: D 67 TYR cc_start: 0.7013 (t80) cc_final: 0.6695 (t80) REVERT: D 83 LEU cc_start: 0.9113 (mt) cc_final: 0.8682 (mm) REVERT: D 96 MET cc_start: 0.9070 (mmt) cc_final: 0.8763 (mmm) REVERT: D 99 MET cc_start: 0.8667 (ptt) cc_final: 0.8421 (ptm) REVERT: D 203 LEU cc_start: 0.9426 (mt) cc_final: 0.9226 (mt) REVERT: D 294 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8778 (mt-10) REVERT: D 300 LYS cc_start: 0.8731 (mppt) cc_final: 0.8195 (mmtt) REVERT: D 315 GLU cc_start: 0.9154 (mp0) cc_final: 0.8696 (mp0) REVERT: D 322 LYS cc_start: 0.9448 (mtpm) cc_final: 0.9157 (mmtt) REVERT: D 435 MET cc_start: 0.9328 (mmm) cc_final: 0.8766 (mmm) REVERT: D 553 PHE cc_start: 0.8688 (t80) cc_final: 0.8453 (t80) REVERT: D 583 TRP cc_start: 0.8875 (t60) cc_final: 0.8388 (t60) REVERT: D 593 TRP cc_start: 0.9463 (t60) cc_final: 0.8603 (t60) outliers start: 64 outliers final: 33 residues processed: 475 average time/residue: 0.1258 time to fit residues: 95.9605 Evaluate side-chains 420 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 385 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 103 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 187 optimal weight: 0.0070 chunk 160 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 133 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 HIS B 40 GLN B 118 GLN C 40 GLN C 310 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.084442 restraints weight = 47985.520| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.42 r_work: 0.3081 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21161 Z= 0.128 Angle : 0.680 8.811 28628 Z= 0.342 Chirality : 0.041 0.239 3196 Planarity : 0.005 0.048 3500 Dihedral : 15.624 138.235 4097 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.40 % Favored : 92.43 % Rotamer: Outliers : 4.06 % Allowed : 15.97 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.74 (0.17), residues: 2432 helix: 0.53 (0.13), residues: 1492 sheet: -5.09 (0.22), residues: 68 loop : -1.85 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 302 TYR 0.021 0.001 TYR D 270 PHE 0.032 0.001 PHE B 434 TRP 0.010 0.001 TRP B 593 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (21161) covalent geometry : angle 0.67980 / 0.34 (28628) hydrogen bonds : bond 0.03947 / 2.66 ( 1013) hydrogen bonds : angle 4.39524 / 3.13 ( 2859) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 443 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8981 (tm-30) REVERT: A 96 MET cc_start: 0.9048 (mmt) cc_final: 0.8840 (mmm) REVERT: A 99 MET cc_start: 0.8605 (ptt) cc_final: 0.8332 (ptm) REVERT: A 300 LYS cc_start: 0.8688 (mppt) cc_final: 0.8327 (mmtt) REVERT: A 307 ILE cc_start: 0.9135 (tp) cc_final: 0.8649 (tp) REVERT: A 315 GLU cc_start: 0.9141 (mp0) cc_final: 0.8673 (mp0) REVERT: A 328 TYR cc_start: 0.9210 (m-80) cc_final: 0.8899 (m-80) REVERT: A 435 MET cc_start: 0.9245 (mmm) cc_final: 0.8506 (mmm) REVERT: A 583 TRP cc_start: 0.8926 (t60) cc_final: 0.8431 (t60) REVERT: A 605 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8739 (pp20) REVERT: B 96 MET cc_start: 0.9092 (mmt) cc_final: 0.8828 (mmm) REVERT: B 99 MET cc_start: 0.8634 (ptt) cc_final: 0.8376 (ptm) REVERT: B 113 GLU cc_start: 0.9011 (pp20) cc_final: 0.8585 (pp20) REVERT: B 215 MET cc_start: 0.9072 (mmp) cc_final: 0.8797 (tpp) REVERT: B 300 LYS cc_start: 0.8816 (mppt) cc_final: 0.8476 (mmtt) REVERT: B 302 ARG cc_start: 0.8390 (mmm160) cc_final: 0.7993 (mmm160) REVERT: B 307 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8600 (tp) REVERT: B 315 GLU cc_start: 0.9142 (mp0) cc_final: 0.8646 (mp0) REVERT: B 322 LYS cc_start: 0.9410 (OUTLIER) cc_final: 0.9206 (mptt) REVERT: B 328 TYR cc_start: 0.9113 (m-10) cc_final: 0.8880 (m-80) REVERT: B 435 MET cc_start: 0.9186 (mmm) cc_final: 0.8376 (mmm) REVERT: B 583 TRP cc_start: 0.8955 (t60) cc_final: 0.8469 (t60) REVERT: C 96 MET cc_start: 0.9125 (mmt) cc_final: 0.8820 (mmm) REVERT: C 99 MET cc_start: 0.8640 (ptt) cc_final: 0.8335 (ptm) REVERT: C 113 GLU cc_start: 0.8930 (pp20) cc_final: 0.8503 (pp20) REVERT: C 298 THR cc_start: 0.9049 (m) cc_final: 0.8810 (t) REVERT: C 300 LYS cc_start: 0.8990 (mppt) cc_final: 0.8593 (mmtt) REVERT: C 315 GLU cc_start: 0.9057 (mp0) cc_final: 0.8672 (mp0) REVERT: C 435 MET cc_start: 0.9265 (mmm) cc_final: 0.8382 (mmm) REVERT: C 483 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8757 (tt0) REVERT: C 491 MET cc_start: 0.8344 (tmm) cc_final: 0.7876 (tpt) REVERT: C 537 PHE cc_start: 0.9240 (t80) cc_final: 0.9034 (t80) REVERT: C 553 PHE cc_start: 0.8746 (t80) cc_final: 0.8404 (t80) REVERT: C 583 TRP cc_start: 0.8948 (t60) cc_final: 0.8331 (t60) REVERT: C 593 TRP cc_start: 0.9456 (t60) cc_final: 0.8646 (t60) REVERT: D 40 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9081 (tm-30) REVERT: D 68 GLU cc_start: 0.8311 (pp20) cc_final: 0.8059 (mm-30) REVERT: D 96 MET cc_start: 0.9066 (mmt) cc_final: 0.8807 (mmm) REVERT: D 99 MET cc_start: 0.8641 (ptt) cc_final: 0.8405 (ptm) REVERT: D 294 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8731 (mt-10) REVERT: D 295 LEU cc_start: 0.9198 (mt) cc_final: 0.8970 (mt) REVERT: D 298 THR cc_start: 0.9074 (m) cc_final: 0.8797 (p) REVERT: D 300 LYS cc_start: 0.8658 (mppt) cc_final: 0.8337 (mmtt) REVERT: D 307 ILE cc_start: 0.9091 (tp) cc_final: 0.8515 (tp) REVERT: D 315 GLU cc_start: 0.9109 (mp0) cc_final: 0.8539 (mp0) REVERT: D 435 MET cc_start: 0.9283 (mmm) cc_final: 0.8422 (mmm) REVERT: D 583 TRP cc_start: 0.8881 (t60) cc_final: 0.8384 (t60) outliers start: 86 outliers final: 44 residues processed: 498 average time/residue: 0.1184 time to fit residues: 96.2873 Evaluate side-chains 437 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 388 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 532 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 182 optimal weight: 10.0000 chunk 187 optimal weight: 0.0870 chunk 231 optimal weight: 0.9990 chunk 69 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN C 36 GLN C 40 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.106487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.081033 restraints weight = 48482.076| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.44 r_work: 0.3002 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21161 Z= 0.176 Angle : 0.710 9.004 28628 Z= 0.354 Chirality : 0.043 0.268 3196 Planarity : 0.004 0.044 3500 Dihedral : 15.379 135.923 4095 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.69 % Favored : 92.15 % Rotamer: Outliers : 4.35 % Allowed : 17.49 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.45 (0.17), residues: 2432 helix: 0.74 (0.13), residues: 1460 sheet: -5.00 (0.21), residues: 76 loop : -1.57 (0.22), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 470 TYR 0.018 0.002 TYR D 67 PHE 0.032 0.002 PHE D 434 TRP 0.023 0.001 TRP B 593 HIS 0.010 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (21161) covalent geometry : angle 0.71038 / 0.35 (28628) hydrogen bonds : bond 0.03884 / 2.62 ( 1013) hydrogen bonds : angle 4.53482 / 3.23 ( 2859) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 389 time to evaluate : 0.690 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 40 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.9124 (tm-30) REVERT: A 96 MET cc_start: 0.9081 (mmt) cc_final: 0.8859 (mmm) REVERT: A 99 MET cc_start: 0.8606 (ptt) cc_final: 0.8348 (ptm) REVERT: A 300 LYS cc_start: 0.8734 (mppt) cc_final: 0.8369 (mmtt) REVERT: A 315 GLU cc_start: 0.9202 (mp0) cc_final: 0.8650 (mp0) REVERT: A 328 TYR cc_start: 0.9266 (m-80) cc_final: 0.9031 (m-80) REVERT: A 435 MET cc_start: 0.9267 (mmm) cc_final: 0.8477 (mmm) REVERT: A 583 TRP cc_start: 0.8920 (t60) cc_final: 0.8432 (t60) REVERT: B 40 GLN cc_start: 0.9451 (OUTLIER) cc_final: 0.8962 (tm-30) REVERT: B 96 MET cc_start: 0.9158 (mmt) cc_final: 0.8951 (mmm) REVERT: B 99 MET cc_start: 0.8699 (ptt) cc_final: 0.8492 (ptm) REVERT: B 113 GLU cc_start: 0.9029 (pp20) cc_final: 0.8582 (pp20) REVERT: B 215 MET cc_start: 0.9074 (mmp) cc_final: 0.8827 (tpp) REVERT: B 300 LYS cc_start: 0.8841 (mppt) cc_final: 0.8482 (mmtt) REVERT: B 302 ARG cc_start: 0.8430 (mmm160) cc_final: 0.7971 (mmm160) REVERT: B 315 GLU cc_start: 0.9176 (mp0) cc_final: 0.8608 (mp0) REVERT: B 322 LYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9238 (mptt) REVERT: B 435 MET cc_start: 0.9252 (mmm) cc_final: 0.8411 (mmm) REVERT: B 583 TRP cc_start: 0.8918 (t60) cc_final: 0.8448 (t60) REVERT: C 36 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: C 96 MET cc_start: 0.9122 (mmt) cc_final: 0.8887 (mmm) REVERT: C 99 MET cc_start: 0.8622 (ptt) cc_final: 0.8353 (ptm) REVERT: C 113 GLU cc_start: 0.8975 (pp20) cc_final: 0.8522 (pp20) REVERT: C 249 VAL cc_start: 0.9390 (t) cc_final: 0.9151 (m) REVERT: C 300 LYS cc_start: 0.8986 (mppt) cc_final: 0.8619 (mmtt) REVERT: C 315 GLU cc_start: 0.9153 (mp0) cc_final: 0.8638 (mp0) REVERT: C 435 MET cc_start: 0.9304 (mmm) cc_final: 0.8444 (mmm) REVERT: C 491 MET cc_start: 0.8325 (tmm) cc_final: 0.7826 (tpt) REVERT: C 583 TRP cc_start: 0.8908 (t60) cc_final: 0.8334 (t60) REVERT: D 40 GLN cc_start: 0.9535 (OUTLIER) cc_final: 0.9173 (tm-30) REVERT: D 83 LEU cc_start: 0.9083 (mt) cc_final: 0.8563 (mm) REVERT: D 96 MET cc_start: 0.9118 (mmt) cc_final: 0.8847 (mmm) REVERT: D 99 MET cc_start: 0.8666 (ptt) cc_final: 0.8455 (ptm) REVERT: D 294 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8771 (mt-10) REVERT: D 295 LEU cc_start: 0.9222 (mt) cc_final: 0.9000 (mt) REVERT: D 298 THR cc_start: 0.9152 (m) cc_final: 0.8876 (p) REVERT: D 300 LYS cc_start: 0.8758 (mppt) cc_final: 0.8342 (mmtt) REVERT: D 315 GLU cc_start: 0.9180 (mp0) cc_final: 0.8659 (mp0) REVERT: D 435 MET cc_start: 0.9336 (mmm) cc_final: 0.8477 (mmm) REVERT: D 583 TRP cc_start: 0.8875 (t60) cc_final: 0.8306 (t60) outliers start: 92 outliers final: 69 residues processed: 448 average time/residue: 0.1139 time to fit residues: 84.1618 Evaluate side-chains 441 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 367 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 466 MET Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 635 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 124 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 36 GLN ** C 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 310 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 = 0.3686 r_free = 0.3686 target = 0.109789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.084545 restraints weight = 47797.274| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 3.42 r_work: 0.3090 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21161 Z= 0.123 Angle : 0.682 8.356 28628 Z= 0.337 Chirality : 0.042 0.265 3196 Planarity : 0.004 0.046 3500 Dihedral : 15.066 136.872 4095 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.24 % Favored : 92.60 % Rotamer: Outliers : 3.88 % Allowed : 18.86 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.66 (0.17), residues: 2432 helix: 0.59 (0.13), residues: 1516 sheet: -4.92 (0.24), residues: 68 loop : -1.88 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 470 TYR 0.018 0.001 TYR D 67 PHE 0.032 0.001 PHE D 434 TRP 0.021 0.001 TRP A 593 HIS 0.007 0.001 HIS B 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (21161) covalent geometry : angle 0.68246 / 0.34 (28628) hydrogen bonds : bond 0.03688 / 2.49 ( 1013) hydrogen bonds : angle 4.37979 / 3.12 ( 2859) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 413 time to evaluate : 0.645 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 40 GLN cc_start: 0.9485 (OUTLIER) cc_final: 0.9163 (tm-30) REVERT: A 83 LEU cc_start: 0.9132 (mt) cc_final: 0.8609 (mm) REVERT: A 99 MET cc_start: 0.8574 (ptt) cc_final: 0.8322 (ptm) REVERT: A 300 LYS cc_start: 0.8652 (mppt) cc_final: 0.8315 (mmtt) REVERT: A 315 GLU cc_start: 0.9143 (mp0) cc_final: 0.8644 (mp0) REVERT: A 328 TYR cc_start: 0.9191 (m-80) cc_final: 0.8966 (m-80) REVERT: A 435 MET cc_start: 0.9183 (mmm) cc_final: 0.8420 (mmm) REVERT: A 583 TRP cc_start: 0.8896 (t60) cc_final: 0.8346 (t60) REVERT: B 36 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8070 (tm-30) REVERT: B 40 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9103 (tm-30) REVERT: B 78 MET cc_start: 0.8661 (mpp) cc_final: 0.8457 (mpp) REVERT: B 110 MET cc_start: 0.8132 (mtm) cc_final: 0.7913 (mtm) REVERT: B 249 VAL cc_start: 0.9390 (t) cc_final: 0.9145 (m) REVERT: B 300 LYS cc_start: 0.8806 (mppt) cc_final: 0.8448 (mmtt) REVERT: B 315 GLU cc_start: 0.9155 (mp0) cc_final: 0.8638 (mp0) REVERT: B 322 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9153 (mptt) REVERT: B 435 MET cc_start: 0.9190 (mmm) cc_final: 0.8381 (mmm) REVERT: B 583 TRP cc_start: 0.8907 (t60) cc_final: 0.8418 (t60) REVERT: B 613 TRP cc_start: 0.8354 (t-100) cc_final: 0.8138 (t-100) REVERT: C 40 GLN cc_start: 0.9429 (OUTLIER) cc_final: 0.9078 (tm-30) REVERT: C 96 MET cc_start: 0.9088 (mmt) cc_final: 0.8846 (mmm) REVERT: C 99 MET cc_start: 0.8570 (ptt) cc_final: 0.8331 (ptm) REVERT: C 300 LYS cc_start: 0.8902 (mppt) cc_final: 0.8563 (mmtt) REVERT: C 315 GLU cc_start: 0.9071 (mp0) cc_final: 0.8689 (mp0) REVERT: C 435 MET cc_start: 0.9233 (mmm) cc_final: 0.8400 (mmm) REVERT: C 483 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8749 (tt0) REVERT: C 491 MET cc_start: 0.8331 (tmm) cc_final: 0.7836 (tpt) REVERT: C 537 PHE cc_start: 0.9281 (t80) cc_final: 0.9043 (t80) REVERT: C 553 PHE cc_start: 0.8705 (t80) cc_final: 0.8411 (t80) REVERT: C 583 TRP cc_start: 0.8893 (t60) cc_final: 0.8336 (t60) REVERT: D 40 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.9194 (tm-30) REVERT: D 83 LEU cc_start: 0.9038 (mt) cc_final: 0.8544 (mm) REVERT: D 96 MET cc_start: 0.9067 (mmt) cc_final: 0.8854 (mmm) REVERT: D 99 MET cc_start: 0.8605 (ptt) cc_final: 0.8389 (ptm) REVERT: D 294 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8793 (mt-10) REVERT: D 300 LYS cc_start: 0.8679 (mppt) cc_final: 0.8297 (mmtt) REVERT: D 315 GLU cc_start: 0.9139 (mp0) cc_final: 0.8693 (mp0) REVERT: D 435 MET cc_start: 0.9253 (mmm) cc_final: 0.8415 (mmm) REVERT: D 583 TRP cc_start: 0.8877 (t60) cc_final: 0.8323 (t60) outliers start: 82 outliers final: 58 residues processed: 467 average time/residue: 0.1227 time to fit residues: 94.9820 Evaluate side-chains 444 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 379 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 483 GLN Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 635 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 27 optimal weight: 6.9990 chunk 181 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 218 optimal weight: 0.3980 chunk 43 optimal weight: 7.9990 chunk 177 optimal weight: 4.9990 chunk 195 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 36 GLN C 36 GLN C 596 GLN D 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.082853 restraints weight = 48380.152| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.38 r_work: 0.3052 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21161 Z= 0.163 Angle : 0.704 10.039 28628 Z= 0.348 Chirality : 0.043 0.291 3196 Planarity : 0.004 0.046 3500 Dihedral : 14.961 134.736 4095 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.69 % Favored : 92.15 % Rotamer: Outliers : 4.40 % Allowed : 19.85 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.55 (0.17), residues: 2432 helix: 0.66 (0.13), residues: 1516 sheet: -4.74 (0.25), residues: 76 loop : -1.78 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 350 TYR 0.018 0.002 TYR D 67 PHE 0.032 0.001 PHE D 434 TRP 0.019 0.001 TRP B 593 HIS 0.008 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (21161) covalent geometry : angle 0.70425 / 0.35 (28628) hydrogen bonds : bond 0.03687 / 2.48 ( 1013) hydrogen bonds : angle 4.46500 / 3.18 ( 2859) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 388 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.9135 (tm-30) REVERT: A 110 MET cc_start: 0.8231 (mtt) cc_final: 0.8006 (mtt) REVERT: A 300 LYS cc_start: 0.8692 (mppt) cc_final: 0.8319 (mmtt) REVERT: A 315 GLU cc_start: 0.9187 (mp0) cc_final: 0.8624 (mp0) REVERT: A 435 MET cc_start: 0.9208 (mmm) cc_final: 0.8486 (mmm) REVERT: A 583 TRP cc_start: 0.8928 (t60) cc_final: 0.8380 (t60) REVERT: B 36 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: B 40 GLN cc_start: 0.9538 (OUTLIER) cc_final: 0.9194 (tm-30) REVERT: B 300 LYS cc_start: 0.8807 (mppt) cc_final: 0.8459 (mmtt) REVERT: B 315 GLU cc_start: 0.9180 (mp0) cc_final: 0.8701 (mp0) REVERT: B 322 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9161 (mptt) REVERT: B 435 MET cc_start: 0.9206 (mmm) cc_final: 0.8445 (mmm) REVERT: B 571 LEU cc_start: 0.9313 (tt) cc_final: 0.9013 (tp) REVERT: B 583 TRP cc_start: 0.8921 (t60) cc_final: 0.8363 (t60) REVERT: C 40 GLN cc_start: 0.9515 (OUTLIER) cc_final: 0.9128 (tm-30) REVERT: C 96 MET cc_start: 0.9064 (mmt) cc_final: 0.8828 (mmm) REVERT: C 99 MET cc_start: 0.8563 (ptt) cc_final: 0.8355 (ptm) REVERT: C 300 LYS cc_start: 0.8891 (mppt) cc_final: 0.8524 (mmtt) REVERT: C 315 GLU cc_start: 0.9135 (mp0) cc_final: 0.8585 (mp0) REVERT: C 435 MET cc_start: 0.9270 (mmm) cc_final: 0.8450 (mmm) REVERT: C 491 MET cc_start: 0.8303 (tmm) cc_final: 0.8064 (tmm) REVERT: C 583 TRP cc_start: 0.8919 (t60) cc_final: 0.8357 (t60) REVERT: D 40 GLN cc_start: 0.9518 (OUTLIER) cc_final: 0.9171 (tm-30) REVERT: D 96 MET cc_start: 0.9089 (mmt) cc_final: 0.8881 (mmm) REVERT: D 99 MET cc_start: 0.8587 (ptt) cc_final: 0.8354 (ptm) REVERT: D 294 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8790 (mt-10) REVERT: D 300 LYS cc_start: 0.8730 (mppt) cc_final: 0.8339 (mmtt) REVERT: D 315 GLU cc_start: 0.9166 (mp0) cc_final: 0.8619 (mp0) REVERT: D 435 MET cc_start: 0.9254 (mmm) cc_final: 0.8382 (mmm) REVERT: D 553 PHE cc_start: 0.8765 (t80) cc_final: 0.8519 (t80) REVERT: D 583 TRP cc_start: 0.8872 (t60) cc_final: 0.8313 (t60) outliers start: 93 outliers final: 68 residues processed: 447 average time/residue: 0.1245 time to fit residues: 91.9095 Evaluate side-chains 444 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 370 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain B residue 36 GLN Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 635 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 178 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 199 optimal weight: 30.0000 chunk 154 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN B 165 HIS C 36 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.108766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.083188 restraints weight = 48146.989| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.38 r_work: 0.3059 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21161 Z= 0.154 Angle : 0.704 9.264 28628 Z= 0.347 Chirality : 0.043 0.306 3196 Planarity : 0.004 0.047 3500 Dihedral : 14.863 133.748 4095 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.69 % Favored : 92.15 % Rotamer: Outliers : 3.97 % Allowed : 20.23 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.56 (0.17), residues: 2432 helix: 0.68 (0.13), residues: 1516 sheet: -4.55 (0.25), residues: 88 loop : -1.82 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.019 0.002 TYR C 67 PHE 0.032 0.001 PHE D 434 TRP 0.020 0.001 TRP D 593 HIS 0.009 0.001 HIS B 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (21161) covalent geometry : angle 0.70356 / 0.35 (28628) hydrogen bonds : bond 0.03704 / 2.49 ( 1013) hydrogen bonds : angle 4.46256 / 3.17 ( 2859) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 375 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.9155 (tm-30) REVERT: A 110 MET cc_start: 0.8252 (mtt) cc_final: 0.8002 (mtt) REVERT: A 300 LYS cc_start: 0.8691 (mppt) cc_final: 0.8313 (mmtt) REVERT: A 315 GLU cc_start: 0.9183 (mp0) cc_final: 0.8589 (mp0) REVERT: A 435 MET cc_start: 0.9219 (mmm) cc_final: 0.8519 (mmm) REVERT: A 583 TRP cc_start: 0.8932 (t60) cc_final: 0.8394 (t60) REVERT: B 40 GLN cc_start: 0.9538 (OUTLIER) cc_final: 0.9120 (tm-30) REVERT: B 78 MET cc_start: 0.8642 (mpp) cc_final: 0.8392 (mpp) REVERT: B 249 VAL cc_start: 0.9440 (t) cc_final: 0.9215 (m) REVERT: B 300 LYS cc_start: 0.8815 (mppt) cc_final: 0.8440 (mmtt) REVERT: B 315 GLU cc_start: 0.9179 (mp0) cc_final: 0.8692 (mp0) REVERT: B 322 LYS cc_start: 0.9392 (OUTLIER) cc_final: 0.9160 (mptt) REVERT: B 328 TYR cc_start: 0.9222 (m-80) cc_final: 0.8969 (m-80) REVERT: B 435 MET cc_start: 0.9194 (mmm) cc_final: 0.8454 (mmm) REVERT: B 583 TRP cc_start: 0.8913 (t60) cc_final: 0.8366 (t60) REVERT: C 40 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9078 (tm-30) REVERT: C 78 MET cc_start: 0.8545 (mpp) cc_final: 0.8180 (mpp) REVERT: C 96 MET cc_start: 0.9032 (mmt) cc_final: 0.8805 (mmm) REVERT: C 300 LYS cc_start: 0.8852 (mppt) cc_final: 0.8490 (mmtt) REVERT: C 315 GLU cc_start: 0.9131 (mp0) cc_final: 0.8577 (mp0) REVERT: C 435 MET cc_start: 0.9261 (mmm) cc_final: 0.8408 (mmm) REVERT: C 491 MET cc_start: 0.8304 (tmm) cc_final: 0.8055 (tmm) REVERT: C 583 TRP cc_start: 0.8908 (t60) cc_final: 0.8358 (t60) REVERT: C 593 TRP cc_start: 0.9474 (t60) cc_final: 0.8615 (t60) REVERT: D 40 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9193 (tm-30) REVERT: D 83 LEU cc_start: 0.8981 (mt) cc_final: 0.8454 (mm) REVERT: D 99 MET cc_start: 0.8614 (ptt) cc_final: 0.8413 (ptm) REVERT: D 300 LYS cc_start: 0.8716 (mppt) cc_final: 0.8333 (mmtt) REVERT: D 315 GLU cc_start: 0.9170 (mp0) cc_final: 0.8618 (mp0) REVERT: D 435 MET cc_start: 0.9261 (mmm) cc_final: 0.8420 (mmm) REVERT: D 583 TRP cc_start: 0.8879 (t60) cc_final: 0.8322 (t60) outliers start: 84 outliers final: 63 residues processed: 430 average time/residue: 0.1249 time to fit residues: 89.1839 Evaluate side-chains 427 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 359 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 635 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 204 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 169 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN B 369 GLN D 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.082177 restraints weight = 48577.170| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.37 r_work: 0.3039 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21161 Z= 0.182 Angle : 0.732 8.929 28628 Z= 0.360 Chirality : 0.045 0.337 3196 Planarity : 0.004 0.047 3500 Dihedral : 14.845 131.970 4095 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.69 % Favored : 92.15 % Rotamer: Outliers : 3.88 % Allowed : 20.84 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.55 (0.17), residues: 2432 helix: 0.68 (0.13), residues: 1516 sheet: -4.61 (0.25), residues: 88 loop : -1.79 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 350 TYR 0.018 0.002 TYR D 67 PHE 0.032 0.001 PHE D 434 TRP 0.019 0.002 TRP B 593 HIS 0.009 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (21161) covalent geometry : angle 0.73163 / 0.36 (28628) hydrogen bonds : bond 0.03760 / 2.52 ( 1013) hydrogen bonds : angle 4.56128 / 3.24 ( 2859) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 366 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.9518 (OUTLIER) cc_final: 0.9117 (tm-30) REVERT: A 83 LEU cc_start: 0.9062 (mt) cc_final: 0.8538 (mm) REVERT: A 300 LYS cc_start: 0.8707 (mppt) cc_final: 0.8312 (mmtt) REVERT: A 315 GLU cc_start: 0.9189 (mp0) cc_final: 0.8666 (mp0) REVERT: A 435 MET cc_start: 0.9231 (mmm) cc_final: 0.8516 (mmm) REVERT: A 583 TRP cc_start: 0.8946 (t60) cc_final: 0.8397 (t60) REVERT: B 40 GLN cc_start: 0.9532 (OUTLIER) cc_final: 0.9165 (tm-30) REVERT: B 249 VAL cc_start: 0.9457 (t) cc_final: 0.9224 (m) REVERT: B 300 LYS cc_start: 0.8810 (mppt) cc_final: 0.8459 (mmtt) REVERT: B 315 GLU cc_start: 0.9189 (mp0) cc_final: 0.8666 (mp0) REVERT: B 322 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9164 (mptt) REVERT: B 328 TYR cc_start: 0.9216 (m-80) cc_final: 0.8981 (m-80) REVERT: B 435 MET cc_start: 0.9203 (mmm) cc_final: 0.8467 (mmm) REVERT: B 583 TRP cc_start: 0.8921 (t60) cc_final: 0.8377 (t60) REVERT: C 40 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9137 (tm-30) REVERT: C 78 MET cc_start: 0.8606 (mpp) cc_final: 0.8360 (mpp) REVERT: C 300 LYS cc_start: 0.8873 (mppt) cc_final: 0.8365 (mmpt) REVERT: C 435 MET cc_start: 0.9264 (mmm) cc_final: 0.8416 (mmm) REVERT: C 491 MET cc_start: 0.8304 (tmm) cc_final: 0.8053 (tmm) REVERT: C 583 TRP cc_start: 0.8930 (t60) cc_final: 0.8390 (t60) REVERT: D 40 GLN cc_start: 0.9513 (OUTLIER) cc_final: 0.9135 (tm-30) REVERT: D 83 LEU cc_start: 0.8975 (mt) cc_final: 0.8472 (mm) REVERT: D 300 LYS cc_start: 0.8736 (mppt) cc_final: 0.8337 (mmtt) REVERT: D 315 GLU cc_start: 0.9191 (mp0) cc_final: 0.8603 (mp0) REVERT: D 435 MET cc_start: 0.9251 (mmm) cc_final: 0.8441 (mmm) REVERT: D 583 TRP cc_start: 0.8882 (t60) cc_final: 0.8342 (t60) outliers start: 82 outliers final: 69 residues processed: 417 average time/residue: 0.1232 time to fit residues: 84.7666 Evaluate side-chains 430 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 356 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 577 MET Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 635 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 162 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 211 optimal weight: 10.0000 chunk 4 optimal weight: 0.0070 chunk 123 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 206 GLN B 36 GLN B 206 GLN B 369 GLN C 206 GLN D 40 GLN D 206 GLN D 513 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.111074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.085671 restraints weight = 47950.268| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.41 r_work: 0.3105 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 21161 Z= 0.125 Angle : 0.714 17.543 28628 Z= 0.347 Chirality : 0.044 0.366 3196 Planarity : 0.004 0.048 3500 Dihedral : 14.515 133.002 4095 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.20 % Favored : 92.64 % Rotamer: Outliers : 3.50 % Allowed : 21.22 % Favored : 75.28 % 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: -0.48 (0.17), residues: 2432 helix: 0.70 (0.13), residues: 1508 sheet: -4.47 (0.26), residues: 88 loop : -1.69 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 350 TYR 0.019 0.001 TYR A 67 PHE 0.033 0.001 PHE B 553 TRP 0.022 0.001 TRP D 593 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (21161) covalent geometry : angle 0.71435 / 0.35 (28628) hydrogen bonds : bond 0.03628 / 2.42 ( 1013) hydrogen bonds : angle 4.44257 / 3.16 ( 2859) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4864 Ramachandran restraints generated. 2432 Oldfield, 0 Emsley, 2432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 401 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.9289 (tm-30) REVERT: A 300 LYS cc_start: 0.8660 (mppt) cc_final: 0.8282 (mmtt) REVERT: A 315 GLU cc_start: 0.9172 (mp0) cc_final: 0.8693 (mp0) REVERT: A 435 MET cc_start: 0.9159 (mmm) cc_final: 0.8454 (mmm) REVERT: A 553 PHE cc_start: 0.8696 (t80) cc_final: 0.8439 (t80) REVERT: A 583 TRP cc_start: 0.8909 (t60) cc_final: 0.8358 (t60) REVERT: B 40 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.9058 (tm-30) REVERT: B 113 GLU cc_start: 0.9175 (pm20) cc_final: 0.8973 (pm20) REVERT: B 300 LYS cc_start: 0.8787 (mppt) cc_final: 0.8403 (mmtt) REVERT: B 315 GLU cc_start: 0.9179 (mp0) cc_final: 0.8730 (mp0) REVERT: B 322 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9106 (mptt) REVERT: B 328 TYR cc_start: 0.9188 (m-80) cc_final: 0.8968 (m-80) REVERT: B 435 MET cc_start: 0.9102 (mmm) cc_final: 0.8398 (mmm) REVERT: B 583 TRP cc_start: 0.8921 (t60) cc_final: 0.8360 (t60) REVERT: C 40 GLN cc_start: 0.9472 (OUTLIER) cc_final: 0.9062 (tm-30) REVERT: C 300 LYS cc_start: 0.8793 (mppt) cc_final: 0.8417 (mmtt) REVERT: C 315 GLU cc_start: 0.9117 (mp0) cc_final: 0.8548 (mp0) REVERT: C 365 ASN cc_start: 0.8282 (t0) cc_final: 0.7710 (t0) REVERT: C 435 MET cc_start: 0.9205 (mmm) cc_final: 0.8383 (mmm) REVERT: C 491 MET cc_start: 0.8302 (tmm) cc_final: 0.8062 (tmm) REVERT: C 583 TRP cc_start: 0.8928 (t60) cc_final: 0.8380 (t60) REVERT: C 593 TRP cc_start: 0.9465 (t60) cc_final: 0.8591 (t60) REVERT: D 40 GLN cc_start: 0.9538 (OUTLIER) cc_final: 0.9301 (tm-30) REVERT: D 83 LEU cc_start: 0.8960 (mt) cc_final: 0.8478 (mm) REVERT: D 300 LYS cc_start: 0.8702 (mppt) cc_final: 0.8312 (mmtt) REVERT: D 315 GLU cc_start: 0.9193 (mp0) cc_final: 0.8649 (mp0) REVERT: D 435 MET cc_start: 0.9179 (mmm) cc_final: 0.8483 (mmm) REVERT: D 553 PHE cc_start: 0.8715 (t80) cc_final: 0.8466 (t80) REVERT: D 583 TRP cc_start: 0.8846 (t60) cc_final: 0.8302 (t60) outliers start: 74 outliers final: 61 residues processed: 451 average time/residue: 0.1224 time to fit residues: 91.2600 Evaluate side-chains 437 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 371 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 165 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain B residue 40 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 165 HIS Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 322 LYS Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 408 PHE Chi-restraints excluded: chain B residue 421 LEU Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 532 SER Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 318 SER Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 635 ASP Chi-restraints excluded: chain D residue 40 GLN Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain D residue 490 LEU Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 635 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 21 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN D 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.107935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082701 restraints weight = 48521.907| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.35 r_work: 0.3040 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3035 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3035 r_free = 0.3035 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3035 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21161 Z= 0.196 Angle : 0.755 16.668 28628 Z= 0.369 Chirality : 0.046 0.351 3196 Planarity : 0.004 0.048 3500 Dihedral : 14.629 129.173 4095 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.94 % Favored : 91.94 % Rotamer: Outliers : 3.59 % Allowed : 21.55 % Favored : 74.86 % 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: -0.48 (0.18), residues: 2432 helix: 0.68 (0.13), residues: 1520 sheet: -4.57 (0.26), residues: 88 loop : -1.66 (0.24), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.018 0.002 TYR D 67 PHE 0.033 0.002 PHE D 434 TRP 0.020 0.002 TRP D 593 HIS 0.011 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (21161) covalent geometry : angle 0.75513 / 0.37 (28628) hydrogen bonds : bond 0.03694 / 2.47 ( 1013) hydrogen bonds : angle 4.60000 / 3.26 ( 2859) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4369.12 seconds wall clock time: 75 minutes 56.79 seconds (4556.79 seconds total)