Starting phenix.real_space_refine on Sat Jul 4 10:49:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ffo_29049/07_2026/8ffo_29049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ffo_29049/07_2026/8ffo_29049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ffo_29049/07_2026/8ffo_29049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ffo_29049/07_2026/8ffo_29049.map" model { file = "/net/cci-nas-00/data/ceres_data/8ffo_29049/07_2026/8ffo_29049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ffo_29049/07_2026/8ffo_29049_neut.cif" } resolution = 3.5 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= 0.040 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 16 5.49 5 S 136 5.16 5 C 13132 2.51 5 N 3272 2.21 5 O 3544 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 20100 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "B" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "C" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "D" Number of atoms: 4839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4839 Classifications: {'peptide': 604} Link IDs: {'PTRANS': 24, 'TRANS': 579} Chain breaks: 2 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3, 'CPL:plan-4': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 4, 'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 4.04, per 1000 atoms: 0.20 Number of scatterers: 20100 At special positions: 0 Unit cell: (136.95, 136.95, 121.18, 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 136 16.00 P 16 15.00 O 3544 8.00 N 3272 7.00 C 13132 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: 1.65 Conformation dependent library (CDL) restraints added in 823.9 milliseconds 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4560 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 12 sheets defined 67.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.584A pdb=" N ARG A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.844A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 101 removed outlier: 3.945A pdb=" N ALA A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.528A pdb=" N LEU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.830A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.555A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 210 through 223 removed outlier: 4.197A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.522A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.594A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.898A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.701A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.504A pdb=" N PHE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.581A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 472 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 4.181A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 4.998A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.681A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.644A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 588 removed outlier: 3.863A pdb=" N ASN A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.584A pdb=" N ARG B 35 " --> pdb=" O GLN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.844A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.945A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.528A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.830A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.555A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 210 through 223 removed outlier: 4.197A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.522A pdb=" N VAL B 235 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.594A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.898A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.701A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 removed outlier: 3.504A pdb=" N PHE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.581A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 487 removed outlier: 4.181A pdb=" N THR B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 4.998A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.681A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.644A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 588 removed outlier: 3.863A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.584A pdb=" N ARG C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.844A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 101 removed outlier: 3.945A pdb=" N ALA C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 108 removed outlier: 3.528A pdb=" N LEU C 105 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.830A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.555A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 210 through 223 removed outlier: 4.197A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.522A pdb=" N VAL C 235 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.594A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.898A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.701A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.504A pdb=" N PHE C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.581A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 removed outlier: 4.181A pdb=" N THR C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE C 480 " --> pdb=" O GLY C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 4.998A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.681A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.644A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 588 removed outlier: 3.863A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU C 588 " --> pdb=" O ARG C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 608 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.584A pdb=" N ARG D 35 " --> pdb=" O GLN D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.844A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.945A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 removed outlier: 3.528A pdb=" N LEU D 105 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.830A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.555A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 210 through 223 removed outlier: 4.197A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.522A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.594A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.898A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.701A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 416 removed outlier: 3.504A pdb=" N PHE D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.581A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 4.181A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.998A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.681A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.644A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 588 removed outlier: 3.863A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 Processing helix chain 'D' and resid 609 through 613 Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 112 removed outlier: 3.848A pdb=" N CYS A 112 " --> pdb=" O PHE A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.803A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 112 removed outlier: 3.848A pdb=" N CYS B 112 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 266 through 270 removed outlier: 6.803A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'C' and resid 111 through 112 removed outlier: 3.848A pdb=" N CYS C 112 " --> pdb=" O PHE C 115 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 266 through 270 removed outlier: 6.803A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AB1, first strand: chain 'D' and resid 111 through 112 removed outlier: 3.848A pdb=" N CYS D 112 " --> pdb=" O PHE D 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 266 through 270 removed outlier: 6.803A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 352 through 354 1097 hydrogen bonds defined for protein. 3135 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: 3.77 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3472 1.33 - 1.45: 5232 1.45 - 1.58: 11580 1.58 - 1.71: 32 1.71 - 1.83: 232 Bond restraints: 20548 Sorted by residual: bond pdb=" O4P CPL C 801 " pdb=" P CPL C 801 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O4P CPL B 801 " pdb=" P CPL B 801 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O4P CPL D 801 " pdb=" P CPL D 801 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" O4P CPL A 807 " pdb=" P CPL A 807 " ideal model delta sigma weight residual 1.648 1.834 -0.186 2.00e-02 2.50e+03 8.63e+01 bond pdb=" C2 CPL A 807 " pdb=" C3 CPL A 807 " ideal model delta sigma weight residual 1.511 1.634 -0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 20543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 27624 2.92 - 5.84: 180 5.84 - 8.76: 40 8.76 - 11.68: 12 11.68 - 14.59: 4 Bond angle restraints: 27860 Sorted by residual: angle pdb=" O3P CPL B 801 " pdb=" P CPL B 801 " pdb=" O4P CPL B 801 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O3P CPL C 801 " pdb=" P CPL C 801 " pdb=" O4P CPL C 801 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O3P CPL D 801 " pdb=" P CPL D 801 " pdb=" O4P CPL D 801 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" O3P CPL A 807 " pdb=" P CPL A 807 " pdb=" O4P CPL A 807 " ideal model delta sigma weight residual 93.29 107.88 -14.59 3.00e+00 1.11e-01 2.37e+01 angle pdb=" C12 CPL C 801 " pdb=" C11 CPL C 801 " pdb=" O3 CPL C 801 " ideal model delta sigma weight residual 111.42 122.50 -11.08 3.00e+00 1.11e-01 1.36e+01 ... (remaining 27855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 12412 34.82 - 69.65: 196 69.65 - 104.47: 16 104.47 - 139.29: 0 139.29 - 174.11: 12 Dihedral angle restraints: 12636 sinusoidal: 5584 harmonic: 7052 Sorted by residual: dihedral pdb=" C3 CPL C 801 " pdb=" C1 CPL C 801 " pdb=" C2 CPL C 801 " pdb=" O3P CPL C 801 " ideal model delta sinusoidal sigma weight residual 72.09 -113.80 -174.11 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL B 801 " pdb=" C1 CPL B 801 " pdb=" C2 CPL B 801 " pdb=" O3P CPL B 801 " ideal model delta sinusoidal sigma weight residual 72.09 -113.80 -174.11 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL D 801 " pdb=" C1 CPL D 801 " pdb=" C2 CPL D 801 " pdb=" O3P CPL D 801 " ideal model delta sinusoidal sigma weight residual 72.09 -113.80 -174.11 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2928 0.075 - 0.149: 204 0.149 - 0.224: 24 0.224 - 0.299: 4 0.299 - 0.374: 4 Chirality restraints: 3164 Sorted by residual: chirality pdb=" C2 CPL A 807 " pdb=" C1 CPL A 807 " pdb=" C3 CPL A 807 " pdb=" O2 CPL A 807 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2 CPL D 801 " pdb=" C1 CPL D 801 " pdb=" C3 CPL D 801 " pdb=" O2 CPL D 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" C2 CPL B 801 " pdb=" C1 CPL B 801 " pdb=" C3 CPL B 801 " pdb=" O2 CPL B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 3161 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG A 805 " -0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C22 ERG A 805 " 0.109 2.00e-02 2.50e+03 pdb=" C23 ERG A 805 " 0.113 2.00e-02 2.50e+03 pdb=" C24 ERG A 805 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 806 " 0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C22 ERG B 806 " -0.109 2.00e-02 2.50e+03 pdb=" C23 ERG B 806 " -0.113 2.00e-02 2.50e+03 pdb=" C24 ERG B 806 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG C 806 " 0.111 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C22 ERG C 806 " -0.109 2.00e-02 2.50e+03 pdb=" C23 ERG C 806 " -0.113 2.00e-02 2.50e+03 pdb=" C24 ERG C 806 " 0.112 2.00e-02 2.50e+03 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5440 2.81 - 3.33: 17983 3.33 - 3.86: 33364 3.86 - 4.38: 39014 4.38 - 4.90: 68483 Nonbonded interactions: 164284 Sorted by model distance: nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.289 3.040 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.289 3.040 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.289 3.040 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR C 336 " pdb=" OG SER C 464 " model vdw 2.318 3.040 ... (remaining 164279 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 638 or resid 803 through 804)) selection = (chain 'B' and (resid 29 through 638 or resid 803 through 804)) selection = (chain 'C' and (resid 29 through 638 or resid 803 through 804)) selection = (chain 'D' and (resid 29 through 638 or resid 803 through 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 17.390 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.186 20548 Z= 0.386 Angle : 0.720 14.594 27860 Z= 0.359 Chirality : 0.044 0.374 3164 Planarity : 0.007 0.111 3428 Dihedral : 13.998 174.114 8076 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.19 % Allowed : 4.21 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.15), residues: 2392 helix: -1.02 (0.11), residues: 1468 sheet: -3.42 (0.36), residues: 124 loop : -1.51 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 584 TYR 0.011 0.001 TYR D 555 PHE 0.012 0.001 PHE B 169 TRP 0.007 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.39 (20548) covalent geometry : angle 0.71994 / 0.36 (27860) hydrogen bonds : bond 0.15563 / 10.55 ( 1097) hydrogen bonds : angle 5.65692 / 3.98 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 504 time to evaluate : 0.916 Fit side-chains REVERT: A 130 LEU cc_start: 0.8959 (tp) cc_final: 0.8712 (tp) REVERT: A 217 ASN cc_start: 0.8431 (t0) cc_final: 0.8218 (m-40) REVERT: A 262 LYS cc_start: 0.9057 (mtpm) cc_final: 0.8812 (mtpp) REVERT: A 340 MET cc_start: 0.8592 (mmm) cc_final: 0.8309 (tpt) REVERT: A 364 ASP cc_start: 0.8531 (t0) cc_final: 0.8253 (t0) REVERT: A 370 GLN cc_start: 0.8231 (mt0) cc_final: 0.8001 (mt0) REVERT: A 474 MET cc_start: 0.6755 (ptp) cc_final: 0.6145 (ptt) REVERT: B 130 LEU cc_start: 0.8964 (tp) cc_final: 0.8714 (tp) REVERT: B 217 ASN cc_start: 0.8430 (t0) cc_final: 0.8218 (m-40) REVERT: B 262 LYS cc_start: 0.9054 (mtpm) cc_final: 0.8809 (mtpp) REVERT: B 340 MET cc_start: 0.8597 (mmm) cc_final: 0.8319 (tpt) REVERT: B 364 ASP cc_start: 0.8531 (t0) cc_final: 0.8255 (t0) REVERT: B 370 GLN cc_start: 0.8233 (mt0) cc_final: 0.8001 (mt0) REVERT: B 474 MET cc_start: 0.6760 (ptp) cc_final: 0.6152 (ptt) REVERT: C 130 LEU cc_start: 0.8968 (tp) cc_final: 0.8717 (tp) REVERT: C 217 ASN cc_start: 0.8432 (t0) cc_final: 0.8216 (m-40) REVERT: C 262 LYS cc_start: 0.9052 (mtpm) cc_final: 0.8808 (mtpp) REVERT: C 340 MET cc_start: 0.8594 (mmm) cc_final: 0.8317 (tpt) REVERT: C 364 ASP cc_start: 0.8529 (t0) cc_final: 0.8253 (t0) REVERT: C 370 GLN cc_start: 0.8228 (mt0) cc_final: 0.8000 (mt0) REVERT: C 474 MET cc_start: 0.6751 (ptp) cc_final: 0.6142 (ptt) REVERT: D 130 LEU cc_start: 0.8965 (tp) cc_final: 0.8712 (tp) REVERT: D 217 ASN cc_start: 0.8430 (t0) cc_final: 0.8217 (m-40) REVERT: D 262 LYS cc_start: 0.9054 (mtpm) cc_final: 0.8808 (mtpp) REVERT: D 340 MET cc_start: 0.8596 (mmm) cc_final: 0.8312 (tpt) REVERT: D 364 ASP cc_start: 0.8528 (t0) cc_final: 0.8249 (t0) REVERT: D 370 GLN cc_start: 0.8234 (mt0) cc_final: 0.8002 (mt0) REVERT: D 474 MET cc_start: 0.6749 (ptp) cc_final: 0.6140 (ptt) outliers start: 4 outliers final: 0 residues processed: 508 average time/residue: 0.1581 time to fit residues: 120.7603 Evaluate side-chains 304 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 185 HIS A 192 GLN A 208 ASN A 310 GLN A 596 GLN B 128 GLN B 185 HIS B 192 GLN B 208 ASN B 310 GLN B 596 GLN C 128 GLN C 185 HIS C 192 GLN C 208 ASN C 214 GLN C 310 GLN C 596 GLN D 128 GLN D 185 HIS D 192 GLN D 208 ASN D 214 GLN D 310 GLN D 596 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.127122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.098575 restraints weight = 24057.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.101034 restraints weight = 16047.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.102703 restraints weight = 12384.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.103741 restraints weight = 10472.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.104344 restraints weight = 9370.663| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20548 Z= 0.110 Angle : 0.497 6.243 27860 Z= 0.251 Chirality : 0.036 0.116 3164 Planarity : 0.004 0.054 3428 Dihedral : 13.694 173.160 3492 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.15 % Allowed : 8.81 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.16), residues: 2392 helix: 0.71 (0.13), residues: 1480 sheet: -3.40 (0.36), residues: 124 loop : -1.01 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.020 0.001 TYR B 621 PHE 0.009 0.001 PHE B 211 TRP 0.007 0.001 TRP D 593 HIS 0.002 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (20548) covalent geometry : angle 0.49719 / 0.25 (27860) hydrogen bonds : bond 0.03686 / 2.47 ( 1097) hydrogen bonds : angle 3.75074 / 2.65 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 0.738 Fit side-chains REVERT: A 195 LEU cc_start: 0.7882 (mp) cc_final: 0.7613 (tp) REVERT: A 217 ASN cc_start: 0.8487 (t0) cc_final: 0.8255 (m-40) REVERT: A 260 MET cc_start: 0.8235 (tpt) cc_final: 0.7964 (mmt) REVERT: A 340 MET cc_start: 0.8596 (mmm) cc_final: 0.8372 (tpt) REVERT: A 474 MET cc_start: 0.6856 (ptp) cc_final: 0.6288 (ptt) REVERT: A 554 MET cc_start: 0.8318 (mmm) cc_final: 0.8044 (mmm) REVERT: A 635 ASN cc_start: 0.8215 (p0) cc_final: 0.8012 (p0) REVERT: B 195 LEU cc_start: 0.7884 (mp) cc_final: 0.7618 (tp) REVERT: B 217 ASN cc_start: 0.8487 (t0) cc_final: 0.8255 (m-40) REVERT: B 260 MET cc_start: 0.8230 (tpt) cc_final: 0.7963 (mmt) REVERT: B 340 MET cc_start: 0.8600 (mmm) cc_final: 0.8391 (tpt) REVERT: B 474 MET cc_start: 0.6865 (ptp) cc_final: 0.6297 (ptt) REVERT: B 554 MET cc_start: 0.8317 (mmm) cc_final: 0.8044 (mmm) REVERT: B 635 ASN cc_start: 0.8223 (p0) cc_final: 0.8017 (p0) REVERT: C 195 LEU cc_start: 0.7875 (mp) cc_final: 0.7607 (tp) REVERT: C 217 ASN cc_start: 0.8484 (t0) cc_final: 0.8250 (m-40) REVERT: C 260 MET cc_start: 0.8228 (tpt) cc_final: 0.7958 (mmt) REVERT: C 340 MET cc_start: 0.8606 (mmm) cc_final: 0.8393 (tpt) REVERT: C 474 MET cc_start: 0.6855 (ptp) cc_final: 0.6284 (ptt) REVERT: C 554 MET cc_start: 0.8309 (mmm) cc_final: 0.8034 (mmm) REVERT: C 635 ASN cc_start: 0.8233 (p0) cc_final: 0.8023 (p0) REVERT: D 195 LEU cc_start: 0.7879 (mp) cc_final: 0.7616 (tp) REVERT: D 217 ASN cc_start: 0.8485 (t0) cc_final: 0.8254 (m-40) REVERT: D 260 MET cc_start: 0.8231 (tpt) cc_final: 0.7956 (mmt) REVERT: D 340 MET cc_start: 0.8589 (mmm) cc_final: 0.8363 (tpt) REVERT: D 474 MET cc_start: 0.6852 (ptp) cc_final: 0.6284 (ptt) REVERT: D 554 MET cc_start: 0.8307 (mmm) cc_final: 0.8033 (mmm) REVERT: D 635 ASN cc_start: 0.8208 (p0) cc_final: 0.8001 (p0) outliers start: 24 outliers final: 16 residues processed: 348 average time/residue: 0.1370 time to fit residues: 74.2487 Evaluate side-chains 287 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 379 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 9.9990 chunk 207 optimal weight: 0.0970 chunk 59 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 GLN A 51 GLN A 208 ASN B 31 GLN B 51 GLN B 208 ASN C 31 GLN C 51 GLN C 208 ASN D 31 GLN D 51 GLN D 208 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.122879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095394 restraints weight = 24506.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.097522 restraints weight = 17363.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.098864 restraints weight = 13867.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.099846 restraints weight = 11962.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100579 restraints weight = 10769.601| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20548 Z= 0.138 Angle : 0.498 6.223 27860 Z= 0.249 Chirality : 0.037 0.132 3164 Planarity : 0.004 0.053 3428 Dihedral : 13.081 173.782 3492 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.30 % Allowed : 9.72 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2392 helix: 1.32 (0.13), residues: 1480 sheet: -3.38 (0.37), residues: 124 loop : -0.76 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 33 TYR 0.018 0.001 TYR A 621 PHE 0.009 0.001 PHE B 611 TRP 0.008 0.001 TRP D 495 HIS 0.002 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (20548) covalent geometry : angle 0.49813 / 0.25 (27860) hydrogen bonds : bond 0.03532 / 2.38 ( 1097) hydrogen bonds : angle 3.59355 / 2.55 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 296 time to evaluate : 0.551 Fit side-chains REVERT: A 195 LEU cc_start: 0.7870 (mp) cc_final: 0.7651 (tp) REVERT: A 217 ASN cc_start: 0.8527 (t0) cc_final: 0.8255 (m-40) REVERT: A 260 MET cc_start: 0.8282 (tpt) cc_final: 0.8075 (mmt) REVERT: A 340 MET cc_start: 0.8579 (mmm) cc_final: 0.8337 (tpt) REVERT: A 474 MET cc_start: 0.6829 (ptp) cc_final: 0.6175 (ptt) REVERT: A 635 ASN cc_start: 0.8313 (p0) cc_final: 0.7840 (p0) REVERT: B 195 LEU cc_start: 0.7863 (mp) cc_final: 0.7656 (tp) REVERT: B 217 ASN cc_start: 0.8525 (t0) cc_final: 0.8259 (m-40) REVERT: B 260 MET cc_start: 0.8280 (tpt) cc_final: 0.8076 (mmt) REVERT: B 340 MET cc_start: 0.8585 (mmm) cc_final: 0.8362 (tpt) REVERT: B 474 MET cc_start: 0.6829 (ptp) cc_final: 0.6178 (ptt) REVERT: B 635 ASN cc_start: 0.8325 (p0) cc_final: 0.7850 (p0) REVERT: C 195 LEU cc_start: 0.7864 (mp) cc_final: 0.7646 (tp) REVERT: C 217 ASN cc_start: 0.8540 (t0) cc_final: 0.8264 (m-40) REVERT: C 260 MET cc_start: 0.8281 (tpt) cc_final: 0.8073 (mmt) REVERT: C 340 MET cc_start: 0.8584 (mmm) cc_final: 0.8356 (tpt) REVERT: C 474 MET cc_start: 0.6822 (ptp) cc_final: 0.6171 (ptt) REVERT: C 635 ASN cc_start: 0.8331 (p0) cc_final: 0.7859 (p0) REVERT: D 195 LEU cc_start: 0.7864 (mp) cc_final: 0.7651 (tp) REVERT: D 217 ASN cc_start: 0.8527 (t0) cc_final: 0.8257 (m-40) REVERT: D 260 MET cc_start: 0.8287 (tpt) cc_final: 0.8070 (mmt) REVERT: D 340 MET cc_start: 0.8576 (mmm) cc_final: 0.8335 (tpt) REVERT: D 474 MET cc_start: 0.6822 (ptp) cc_final: 0.6169 (ptt) REVERT: D 635 ASN cc_start: 0.8313 (p0) cc_final: 0.7841 (p0) outliers start: 48 outliers final: 36 residues processed: 336 average time/residue: 0.1321 time to fit residues: 70.3241 Evaluate side-chains 316 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 616 SER Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 616 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 616 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 171 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN B 208 ASN C 208 ASN D 208 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.094875 restraints weight = 24669.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.096986 restraints weight = 17255.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.098451 restraints weight = 13632.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.099310 restraints weight = 11723.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.099997 restraints weight = 10601.772| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20548 Z= 0.132 Angle : 0.482 6.166 27860 Z= 0.241 Chirality : 0.037 0.146 3164 Planarity : 0.004 0.052 3428 Dihedral : 12.880 173.591 3492 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.49 % Allowed : 10.68 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.17), residues: 2392 helix: 1.61 (0.13), residues: 1488 sheet: -3.29 (0.39), residues: 124 loop : -0.61 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 363 TYR 0.017 0.001 TYR C 621 PHE 0.009 0.001 PHE C 169 TRP 0.008 0.001 TRP D 495 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (20548) covalent geometry : angle 0.48224 / 0.24 (27860) hydrogen bonds : bond 0.03434 / 2.31 ( 1097) hydrogen bonds : angle 3.53380 / 2.51 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 296 time to evaluate : 0.637 Fit side-chains REVERT: A 217 ASN cc_start: 0.8533 (t0) cc_final: 0.8290 (m-40) REVERT: A 340 MET cc_start: 0.8582 (mmm) cc_final: 0.8342 (tpt) REVERT: A 474 MET cc_start: 0.6816 (ptp) cc_final: 0.6386 (ptt) REVERT: A 635 ASN cc_start: 0.8400 (p0) cc_final: 0.8072 (p0) REVERT: B 217 ASN cc_start: 0.8530 (t0) cc_final: 0.8296 (m-40) REVERT: B 340 MET cc_start: 0.8590 (mmm) cc_final: 0.8364 (tpt) REVERT: B 474 MET cc_start: 0.6818 (ptp) cc_final: 0.6391 (ptt) REVERT: B 635 ASN cc_start: 0.8407 (p0) cc_final: 0.8085 (p0) REVERT: C 217 ASN cc_start: 0.8559 (t0) cc_final: 0.8311 (m-40) REVERT: C 340 MET cc_start: 0.8587 (mmm) cc_final: 0.8359 (tpt) REVERT: C 474 MET cc_start: 0.6817 (ptp) cc_final: 0.6388 (ptt) REVERT: C 635 ASN cc_start: 0.8418 (p0) cc_final: 0.8097 (p0) REVERT: D 217 ASN cc_start: 0.8535 (t0) cc_final: 0.8293 (m-40) REVERT: D 340 MET cc_start: 0.8577 (mmm) cc_final: 0.8337 (tpt) REVERT: D 474 MET cc_start: 0.6808 (ptp) cc_final: 0.6378 (ptt) REVERT: D 635 ASN cc_start: 0.8399 (p0) cc_final: 0.8072 (p0) outliers start: 52 outliers final: 36 residues processed: 340 average time/residue: 0.1326 time to fit residues: 71.6675 Evaluate side-chains 320 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 394 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 ASN A 208 ASN B 91 ASN B 208 ASN C 91 ASN C 208 ASN D 91 ASN D 208 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.123660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.095194 restraints weight = 24238.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.097705 restraints weight = 16144.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.099344 restraints weight = 12428.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.100487 restraints weight = 10475.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.101091 restraints weight = 9344.848| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20548 Z= 0.109 Angle : 0.467 6.568 27860 Z= 0.234 Chirality : 0.036 0.153 3164 Planarity : 0.004 0.050 3428 Dihedral : 12.729 172.902 3492 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.11 % Allowed : 11.25 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.17), residues: 2392 helix: 1.80 (0.13), residues: 1492 sheet: -3.29 (0.39), residues: 124 loop : -0.49 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 59 TYR 0.014 0.001 TYR A 621 PHE 0.010 0.001 PHE B 611 TRP 0.007 0.001 TRP D 495 HIS 0.002 0.000 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (20548) covalent geometry : angle 0.46747 / 0.23 (27860) hydrogen bonds : bond 0.03276 / 2.20 ( 1097) hydrogen bonds : angle 3.48824 / 2.48 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 0.759 Fit side-chains REVERT: A 217 ASN cc_start: 0.8516 (t0) cc_final: 0.8264 (m-40) REVERT: A 340 MET cc_start: 0.8535 (mmm) cc_final: 0.8326 (tpt) REVERT: A 474 MET cc_start: 0.6835 (ptp) cc_final: 0.6359 (ptt) REVERT: A 635 ASN cc_start: 0.8423 (p0) cc_final: 0.8106 (p0) REVERT: B 217 ASN cc_start: 0.8513 (t0) cc_final: 0.8264 (m-40) REVERT: B 474 MET cc_start: 0.6839 (ptp) cc_final: 0.6365 (ptt) REVERT: B 635 ASN cc_start: 0.8429 (p0) cc_final: 0.8121 (p0) REVERT: C 217 ASN cc_start: 0.8542 (t0) cc_final: 0.8280 (m-40) REVERT: C 474 MET cc_start: 0.6831 (ptp) cc_final: 0.6357 (ptt) REVERT: C 635 ASN cc_start: 0.8437 (p0) cc_final: 0.8125 (p0) REVERT: D 217 ASN cc_start: 0.8517 (t0) cc_final: 0.8259 (m-40) REVERT: D 340 MET cc_start: 0.8531 (mmm) cc_final: 0.8323 (tpt) REVERT: D 474 MET cc_start: 0.6827 (ptp) cc_final: 0.6353 (ptt) REVERT: D 635 ASN cc_start: 0.8414 (p0) cc_final: 0.8096 (p0) outliers start: 44 outliers final: 32 residues processed: 338 average time/residue: 0.1429 time to fit residues: 75.4529 Evaluate side-chains 316 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 GLN A 208 ASN A 582 HIS B 74 GLN B 208 ASN B 582 HIS C 74 GLN C 208 ASN C 582 HIS D 74 GLN D 208 ASN D 582 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.090379 restraints weight = 24749.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.092872 restraints weight = 16076.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.094635 restraints weight = 12250.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095686 restraints weight = 10282.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.096463 restraints weight = 9172.352| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20548 Z= 0.202 Angle : 0.542 6.379 27860 Z= 0.274 Chirality : 0.040 0.178 3164 Planarity : 0.004 0.050 3428 Dihedral : 12.903 172.526 3492 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.39 % Allowed : 12.45 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.17), residues: 2392 helix: 1.61 (0.13), residues: 1488 sheet: -3.31 (0.40), residues: 124 loop : -0.50 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 59 TYR 0.014 0.002 TYR B 555 PHE 0.012 0.001 PHE A 169 TRP 0.009 0.001 TRP B 495 HIS 0.002 0.001 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.20 (20548) covalent geometry : angle 0.54244 / 0.27 (27860) hydrogen bonds : bond 0.03780 / 2.55 ( 1097) hydrogen bonds : angle 3.64583 / 2.59 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.760 Fit side-chains REVERT: A 160 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8676 (pp) REVERT: A 217 ASN cc_start: 0.8564 (t0) cc_final: 0.8261 (m-40) REVERT: A 340 MET cc_start: 0.8587 (mmm) cc_final: 0.8384 (tpt) REVERT: A 474 MET cc_start: 0.7036 (ptp) cc_final: 0.6452 (ptt) REVERT: B 160 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8670 (pp) REVERT: B 217 ASN cc_start: 0.8563 (t0) cc_final: 0.8264 (m-40) REVERT: B 474 MET cc_start: 0.7039 (ptp) cc_final: 0.6454 (ptt) REVERT: C 160 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8675 (pp) REVERT: C 217 ASN cc_start: 0.8581 (t0) cc_final: 0.8272 (m-40) REVERT: C 474 MET cc_start: 0.7034 (ptp) cc_final: 0.6445 (ptt) REVERT: D 160 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8678 (pp) REVERT: D 217 ASN cc_start: 0.8566 (t0) cc_final: 0.8263 (m-40) REVERT: D 340 MET cc_start: 0.8580 (mmm) cc_final: 0.8377 (tpt) REVERT: D 474 MET cc_start: 0.7032 (ptp) cc_final: 0.6449 (ptt) outliers start: 50 outliers final: 30 residues processed: 318 average time/residue: 0.1318 time to fit residues: 66.7075 Evaluate side-chains 298 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ARG Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 45 ARG Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 208 ASN Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 394 THR Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 56 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 6 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 ASN A 369 GLN B 208 ASN B 369 GLN C 208 ASN C 369 GLN D 208 ASN D 369 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.121751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.094165 restraints weight = 24520.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.096384 restraints weight = 16783.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.097932 restraints weight = 13109.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.098919 restraints weight = 11086.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.099534 restraints weight = 9987.929| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20548 Z= 0.109 Angle : 0.482 6.979 27860 Z= 0.241 Chirality : 0.037 0.200 3164 Planarity : 0.003 0.049 3428 Dihedral : 12.732 171.934 3492 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.11 % Allowed : 13.41 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2392 helix: 1.85 (0.13), residues: 1492 sheet: -3.29 (0.40), residues: 124 loop : -0.44 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.015 0.001 TYR B 555 PHE 0.010 0.001 PHE A 611 TRP 0.008 0.001 TRP B 495 HIS 0.002 0.000 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (20548) covalent geometry : angle 0.48187 / 0.24 (27860) hydrogen bonds : bond 0.03359 / 2.25 ( 1097) hydrogen bonds : angle 3.50447 / 2.49 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 274 time to evaluate : 0.746 Fit side-chains REVERT: A 160 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8789 (pp) REVERT: A 217 ASN cc_start: 0.8512 (t0) cc_final: 0.8287 (m-40) REVERT: A 222 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.6728 (t80) REVERT: A 474 MET cc_start: 0.6937 (ptp) cc_final: 0.6414 (ptt) REVERT: B 160 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B 217 ASN cc_start: 0.8510 (t0) cc_final: 0.8290 (m-40) REVERT: B 222 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.6718 (t80) REVERT: B 474 MET cc_start: 0.6935 (ptp) cc_final: 0.6415 (ptt) REVERT: C 160 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8793 (pp) REVERT: C 217 ASN cc_start: 0.8539 (t0) cc_final: 0.8306 (m-40) REVERT: C 222 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.6722 (t80) REVERT: C 474 MET cc_start: 0.6931 (ptp) cc_final: 0.6407 (ptt) REVERT: D 160 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8793 (pp) REVERT: D 217 ASN cc_start: 0.8516 (t0) cc_final: 0.8288 (m-40) REVERT: D 222 TYR cc_start: 0.8096 (OUTLIER) cc_final: 0.6725 (t80) REVERT: D 474 MET cc_start: 0.6928 (ptp) cc_final: 0.6405 (ptt) outliers start: 44 outliers final: 24 residues processed: 310 average time/residue: 0.1445 time to fit residues: 70.5782 Evaluate side-chains 286 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 118 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 26 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 218 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.123133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094332 restraints weight = 24268.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.097013 restraints weight = 15577.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098742 restraints weight = 11753.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.099974 restraints weight = 9794.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.100797 restraints weight = 8639.105| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20548 Z= 0.108 Angle : 0.481 7.205 27860 Z= 0.238 Chirality : 0.037 0.205 3164 Planarity : 0.003 0.049 3428 Dihedral : 12.561 170.129 3492 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.92 % Allowed : 13.75 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2392 helix: 1.93 (0.13), residues: 1492 sheet: -3.22 (0.41), residues: 124 loop : -0.47 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.015 0.001 TYR B 555 PHE 0.009 0.001 PHE C 169 TRP 0.007 0.001 TRP B 495 HIS 0.002 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (20548) covalent geometry : angle 0.48075 / 0.24 (27860) hydrogen bonds : bond 0.03194 / 2.15 ( 1097) hydrogen bonds : angle 3.46965 / 2.47 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.694 Fit side-chains REVERT: A 160 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8695 (pp) REVERT: A 217 ASN cc_start: 0.8518 (t0) cc_final: 0.8231 (m-40) REVERT: A 222 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.6790 (t80) REVERT: A 302 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7948 (ttt-90) REVERT: A 474 MET cc_start: 0.6991 (ptp) cc_final: 0.6413 (ptt) REVERT: B 160 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8693 (pp) REVERT: B 217 ASN cc_start: 0.8515 (t0) cc_final: 0.8231 (m-40) REVERT: B 222 TYR cc_start: 0.8110 (OUTLIER) cc_final: 0.6786 (t80) REVERT: B 302 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7949 (ttt-90) REVERT: B 474 MET cc_start: 0.6991 (ptp) cc_final: 0.6416 (ptt) REVERT: C 160 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8692 (pp) REVERT: C 217 ASN cc_start: 0.8538 (t0) cc_final: 0.8241 (m-40) REVERT: C 222 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6790 (t80) REVERT: C 302 ARG cc_start: 0.8183 (ttp80) cc_final: 0.7944 (ttt-90) REVERT: C 474 MET cc_start: 0.6987 (ptp) cc_final: 0.6413 (ptt) REVERT: D 160 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8697 (pp) REVERT: D 217 ASN cc_start: 0.8515 (t0) cc_final: 0.8223 (m-40) REVERT: D 222 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6789 (t80) REVERT: D 302 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7943 (ttt-90) REVERT: D 474 MET cc_start: 0.6990 (ptp) cc_final: 0.6410 (ptt) outliers start: 40 outliers final: 32 residues processed: 303 average time/residue: 0.1443 time to fit residues: 69.6550 Evaluate side-chains 300 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 185 HIS Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 185 HIS Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 8 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 238 optimal weight: 0.0270 chunk 174 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 157 optimal weight: 0.9990 chunk 139 optimal weight: 0.2980 chunk 164 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 636 HIS B 636 HIS C 636 HIS D 636 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.125519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.097907 restraints weight = 24020.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.100309 restraints weight = 16245.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101944 restraints weight = 12587.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.102975 restraints weight = 10671.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.103630 restraints weight = 9541.695| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20548 Z= 0.094 Angle : 0.487 7.487 27860 Z= 0.237 Chirality : 0.036 0.214 3164 Planarity : 0.003 0.049 3428 Dihedral : 12.395 169.245 3492 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.49 % Allowed : 13.41 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2392 helix: 1.97 (0.13), residues: 1516 sheet: -3.21 (0.41), residues: 124 loop : -0.53 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.013 0.001 TYR D 555 PHE 0.008 0.001 PHE C 611 TRP 0.006 0.001 TRP B 495 HIS 0.001 0.000 HIS D 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 (20548) covalent geometry : angle 0.48694 / 0.24 (27860) hydrogen bonds : bond 0.02999 / 2.01 ( 1097) hydrogen bonds : angle 3.43561 / 2.44 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 0.642 Fit side-chains REVERT: A 160 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8679 (pp) REVERT: A 217 ASN cc_start: 0.8508 (t0) cc_final: 0.8215 (m-40) REVERT: A 222 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6836 (t80) REVERT: A 302 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7872 (ttt-90) REVERT: A 414 ARG cc_start: 0.7937 (tpp-160) cc_final: 0.7601 (mmt180) REVERT: A 474 MET cc_start: 0.6938 (ptp) cc_final: 0.6385 (ptt) REVERT: A 635 ASN cc_start: 0.8457 (p0) cc_final: 0.8108 (p0) REVERT: B 160 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8681 (pp) REVERT: B 217 ASN cc_start: 0.8506 (t0) cc_final: 0.8217 (m-40) REVERT: B 222 TYR cc_start: 0.8088 (OUTLIER) cc_final: 0.6832 (t80) REVERT: B 302 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7873 (ttt-90) REVERT: B 414 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7601 (mmt180) REVERT: B 474 MET cc_start: 0.6943 (ptp) cc_final: 0.6385 (ptt) REVERT: B 635 ASN cc_start: 0.8465 (p0) cc_final: 0.8119 (p0) REVERT: C 160 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8682 (pp) REVERT: C 217 ASN cc_start: 0.8534 (t0) cc_final: 0.8231 (m-40) REVERT: C 222 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6834 (t80) REVERT: C 302 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7870 (ttt-90) REVERT: C 414 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7606 (mmt180) REVERT: C 474 MET cc_start: 0.6939 (ptp) cc_final: 0.6382 (ptt) REVERT: C 635 ASN cc_start: 0.8463 (p0) cc_final: 0.8119 (p0) REVERT: D 160 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8682 (pp) REVERT: D 217 ASN cc_start: 0.8515 (t0) cc_final: 0.8217 (m-40) REVERT: D 222 TYR cc_start: 0.8095 (OUTLIER) cc_final: 0.6838 (t80) REVERT: D 302 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7867 (ttt-90) REVERT: D 414 ARG cc_start: 0.7929 (tpp-160) cc_final: 0.7592 (mmt180) REVERT: D 474 MET cc_start: 0.6939 (ptp) cc_final: 0.6384 (ptt) REVERT: D 635 ASN cc_start: 0.8461 (p0) cc_final: 0.8114 (p0) outliers start: 52 outliers final: 24 residues processed: 339 average time/residue: 0.1352 time to fit residues: 73.0124 Evaluate side-chains 311 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 55 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 223 optimal weight: 0.6980 chunk 72 optimal weight: 0.0060 overall best weight: 1.1400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN A 51 GLN A 185 HIS B 51 GLN B 185 HIS C 51 GLN C 185 HIS D 51 GLN D 185 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.096315 restraints weight = 24201.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098660 restraints weight = 16442.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100221 restraints weight = 12816.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.101176 restraints weight = 10918.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.101888 restraints weight = 9813.227| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20548 Z= 0.122 Angle : 0.508 8.652 27860 Z= 0.248 Chirality : 0.037 0.212 3164 Planarity : 0.003 0.049 3428 Dihedral : 12.412 169.021 3492 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.72 % Allowed : 14.46 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.17), residues: 2392 helix: 1.99 (0.13), residues: 1492 sheet: -3.21 (0.41), residues: 124 loop : -0.57 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 33 TYR 0.014 0.001 TYR D 555 PHE 0.009 0.001 PHE A 169 TRP 0.007 0.001 TRP C 495 HIS 0.002 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (20548) covalent geometry : angle 0.50798 / 0.25 (27860) hydrogen bonds : bond 0.03161 / 2.12 ( 1097) hydrogen bonds : angle 3.49088 / 2.48 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.735 Fit side-chains REVERT: A 160 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8725 (pp) REVERT: A 217 ASN cc_start: 0.8525 (t0) cc_final: 0.8220 (m-40) REVERT: A 222 TYR cc_start: 0.8120 (OUTLIER) cc_final: 0.6873 (t80) REVERT: A 302 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7910 (ttt-90) REVERT: A 340 MET cc_start: 0.8194 (mmt) cc_final: 0.7916 (mmt) REVERT: A 414 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7481 (mmt-90) REVERT: A 474 MET cc_start: 0.6980 (ptp) cc_final: 0.6407 (ptt) REVERT: B 160 ILE cc_start: 0.9000 (OUTLIER) cc_final: 0.8727 (pp) REVERT: B 217 ASN cc_start: 0.8523 (t0) cc_final: 0.8223 (m-40) REVERT: B 222 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.6870 (t80) REVERT: B 302 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7908 (ttt-90) REVERT: B 414 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7475 (mmt-90) REVERT: B 474 MET cc_start: 0.6985 (ptp) cc_final: 0.6428 (ptt) REVERT: B 635 ASN cc_start: 0.8498 (p0) cc_final: 0.8147 (p0) REVERT: C 160 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8732 (pp) REVERT: C 217 ASN cc_start: 0.8546 (t0) cc_final: 0.8236 (m-40) REVERT: C 222 TYR cc_start: 0.8122 (OUTLIER) cc_final: 0.6869 (t80) REVERT: C 302 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7908 (ttt-90) REVERT: C 414 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7472 (mmt-90) REVERT: C 474 MET cc_start: 0.6982 (ptp) cc_final: 0.6421 (ptt) REVERT: C 635 ASN cc_start: 0.8497 (p0) cc_final: 0.8148 (p0) REVERT: D 160 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8736 (pp) REVERT: D 217 ASN cc_start: 0.8530 (t0) cc_final: 0.8222 (m-40) REVERT: D 222 TYR cc_start: 0.8125 (OUTLIER) cc_final: 0.6873 (t80) REVERT: D 302 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7906 (ttt-90) REVERT: D 340 MET cc_start: 0.8194 (mmt) cc_final: 0.7897 (mmt) REVERT: D 414 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7470 (mmt-90) REVERT: D 474 MET cc_start: 0.6978 (ptp) cc_final: 0.6406 (ptt) REVERT: D 635 ASN cc_start: 0.8491 (p0) cc_final: 0.8141 (p0) outliers start: 36 outliers final: 24 residues processed: 297 average time/residue: 0.1418 time to fit residues: 66.5113 Evaluate side-chains 298 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 222 TYR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 222 TYR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 410 VAL Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 222 TYR Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 410 VAL Chi-restraints excluded: chain D residue 501 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 182 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 187 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 222 optimal weight: 0.8980 chunk 175 optimal weight: 0.6980 chunk 64 optimal weight: 7.9990 chunk 139 optimal weight: 0.0050 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.125988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.098737 restraints weight = 24007.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.101016 restraints weight = 16389.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.102472 restraints weight = 12760.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.103616 restraints weight = 10847.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104240 restraints weight = 9759.930| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20548 Z= 0.099 Angle : 0.486 7.602 27860 Z= 0.238 Chirality : 0.036 0.214 3164 Planarity : 0.003 0.049 3428 Dihedral : 12.308 168.448 3492 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.72 % Allowed : 14.51 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.17), residues: 2392 helix: 2.09 (0.13), residues: 1492 sheet: -3.15 (0.43), residues: 124 loop : -0.56 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 33 TYR 0.013 0.001 TYR C 555 PHE 0.011 0.001 PHE D 611 TRP 0.008 0.001 TRP B 462 HIS 0.002 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (20548) covalent geometry : angle 0.48603 / 0.24 (27860) hydrogen bonds : bond 0.03023 / 2.03 ( 1097) hydrogen bonds : angle 3.42789 / 2.44 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3194.00 seconds wall clock time: 56 minutes 6.72 seconds (3366.72 seconds total)