Starting phenix.real_space_refine on Mon Sep 14 09:20:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.map" model { file = "/net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6z16_11027/09_2026/6z16_11027.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 4 8.98 5 P 26 5.49 5 S 142 5.16 5 C 20386 2.51 5 N 4594 2.21 5 O 5098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30250 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6221 Classifications: {'peptide': 788} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 758} Chain: "B" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "D" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3796 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 470} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 648 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "a" Number of atoms: 6221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 788, 6221 Classifications: {'peptide': 788} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 758} Chain: "b" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1070 Classifications: {'peptide': 138} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 132} Chain: "c" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "d" Number of atoms: 3796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3796 Classifications: {'peptide': 489} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 470} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain: "f" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 648 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "g" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "A" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 276 Unusual residues: {' K': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "a" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 276 Unusual residues: {' K': 1, 'PTY': 7} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 75 Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 6.78, per 1000 atoms: 0.22 Number of scatterers: 30250 At special positions: 0 Unit cell: (221.76, 225.12, 95.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 142 16.00 P 26 15.00 O 5098 8.00 N 4594 7.00 C 20386 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: 2.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6960 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 8 sheets defined 78.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.529A pdb=" N PHE A 36 " --> pdb=" O HIS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.553A pdb=" N LEU A 40 " --> pdb=" O PHE A 36 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 56 through 62 removed outlier: 4.257A pdb=" N PHE A 60 " --> pdb=" O HIS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 73 removed outlier: 3.946A pdb=" N ILE A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 4.011A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 Processing helix chain 'A' and resid 135 through 156 removed outlier: 3.872A pdb=" N PHE A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.675A pdb=" N ALA A 178 " --> pdb=" O PHE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 215 removed outlier: 3.683A pdb=" N ARG A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.615A pdb=" N VAL A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'A' and resid 253 through 258 removed outlier: 4.074A pdb=" N ILE A 256 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TRP A 257 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 258 " --> pdb=" O TYR A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 260 through 264 removed outlier: 4.064A pdb=" N GLU A 263 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 264 " --> pdb=" O ALA A 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 260 through 264' Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 279 through 293 Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 295 through 317 removed outlier: 4.027A pdb=" N VAL A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 348 removed outlier: 3.567A pdb=" N ILE A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 removed outlier: 3.933A pdb=" N GLY A 355 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 392 removed outlier: 3.792A pdb=" N VAL A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A 375 " --> pdb=" O PHE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.599A pdb=" N SER A 431 " --> pdb=" O ASN A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'A' and resid 450 through 473 removed outlier: 4.669A pdb=" N VAL A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 455 " --> pdb=" O ILE A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 512 removed outlier: 3.628A pdb=" N LEU A 496 " --> pdb=" O PRO A 492 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ALA A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.544A pdb=" N SER A 517 " --> pdb=" O PRO A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.534A pdb=" N ALA A 524 " --> pdb=" O VAL A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 removed outlier: 3.827A pdb=" N ASP A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 568 removed outlier: 3.817A pdb=" N MET A 555 " --> pdb=" O PRO A 551 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.850A pdb=" N MET A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.579A pdb=" N TYR A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 635 removed outlier: 3.678A pdb=" N TYR A 616 " --> pdb=" O SER A 612 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS A 635 " --> pdb=" O THR A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 668 Processing helix chain 'A' and resid 671 through 693 removed outlier: 3.831A pdb=" N ALA A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 718 removed outlier: 3.547A pdb=" N TYR A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 756 Processing helix chain 'A' and resid 764 through 770 Processing helix chain 'A' and resid 780 through 787 Processing helix chain 'A' and resid 792 through 813 Processing helix chain 'B' and resid 5 through 29 Proline residue: B 17 - end of helix Processing helix chain 'B' and resid 36 through 55 Processing helix chain 'B' and resid 57 through 64 removed outlier: 3.675A pdb=" N ARG B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 89 removed outlier: 3.794A pdb=" N LEU B 71 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 138 removed outlier: 3.604A pdb=" N PHE B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.986A pdb=" N CYS C 11 " --> pdb=" O VAL C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 48 removed outlier: 3.522A pdb=" N ILE C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 98 removed outlier: 4.596A pdb=" N GLN C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 5 removed outlier: 4.214A pdb=" N LEU D 5 " --> pdb=" O SER D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 Proline residue: D 12 - end of helix Processing helix chain 'D' and resid 25 through 54 removed outlier: 3.531A pdb=" N ASP D 54 " --> pdb=" O ARG D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 100 Processing helix chain 'D' and resid 101 through 107 removed outlier: 3.651A pdb=" N GLU D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE D 107 " --> pdb=" O LYS D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 125 removed outlier: 3.514A pdb=" N THR D 125 " --> pdb=" O ASN D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 149 Processing helix chain 'D' and resid 152 through 184 Processing helix chain 'D' and resid 188 through 199 Processing helix chain 'D' and resid 202 through 220 removed outlier: 4.046A pdb=" N THR D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 235 Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 248 through 263 removed outlier: 4.157A pdb=" N GLY D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 removed outlier: 4.289A pdb=" N THR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 293 " --> pdb=" O GLY D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 316 Processing helix chain 'D' and resid 319 through 352 Processing helix chain 'D' and resid 355 through 359 removed outlier: 3.736A pdb=" N PHE D 359 " --> pdb=" O ILE D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 382 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 402 Processing helix chain 'D' and resid 404 through 430 removed outlier: 3.513A pdb=" N ALA D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 462 removed outlier: 4.129A pdb=" N VAL D 449 " --> pdb=" O ARG D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 478 removed outlier: 3.512A pdb=" N VAL D 466 " --> pdb=" O GLY D 462 " (cutoff:3.500A) Proline residue: D 468 - end of helix Processing helix chain 'D' and resid 480 through 488 removed outlier: 3.563A pdb=" N LEU D 488 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 removed outlier: 3.523A pdb=" N THR E 19 " --> pdb=" O TRP E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 41 Processing helix chain 'E' and resid 50 through 80 removed outlier: 3.711A pdb=" N VAL E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 112 removed outlier: 3.715A pdb=" N LEU E 112 " --> pdb=" O MET E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 157 removed outlier: 3.572A pdb=" N SER E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 23 Processing helix chain 'F' and resid 26 through 53 removed outlier: 4.352A pdb=" N ARG F 30 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 80 removed outlier: 3.538A pdb=" N ILE F 61 " --> pdb=" O PHE F 57 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 80 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 34 Processing helix chain 'G' and resid 36 through 67 removed outlier: 3.503A pdb=" N ASN G 67 " --> pdb=" O PHE G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 99 removed outlier: 4.195A pdb=" N LEU G 75 " --> pdb=" O ASN G 71 " (cutoff:3.500A) Proline residue: G 86 - end of helix Processing helix chain 'a' and resid 31 through 36 removed outlier: 3.547A pdb=" N PHE a 36 " --> pdb=" O HIS a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 52 removed outlier: 3.529A pdb=" N LEU a 40 " --> pdb=" O PHE a 36 " (cutoff:3.500A) Proline residue: a 46 - end of helix Processing helix chain 'a' and resid 56 through 62 removed outlier: 4.277A pdb=" N PHE a 60 " --> pdb=" O HIS a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 73 removed outlier: 3.942A pdb=" N ILE a 66 " --> pdb=" O PHE a 62 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 81 removed outlier: 3.897A pdb=" N ASN a 81 " --> pdb=" O ASP a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 129 Processing helix chain 'a' and resid 135 through 156 removed outlier: 3.909A pdb=" N PHE a 139 " --> pdb=" O PRO a 135 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 178 removed outlier: 3.675A pdb=" N ALA a 178 " --> pdb=" O PHE a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 215 removed outlier: 3.750A pdb=" N ARG a 187 " --> pdb=" O ARG a 183 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 224 removed outlier: 3.525A pdb=" N VAL a 224 " --> pdb=" O ILE a 220 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 249 removed outlier: 3.525A pdb=" N SER a 249 " --> pdb=" O ALA a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 253 through 257 removed outlier: 4.122A pdb=" N ILE a 256 " --> pdb=" O PRO a 253 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TRP a 257 " --> pdb=" O PHE a 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 253 through 257' Processing helix chain 'a' and resid 260 through 264 removed outlier: 4.033A pdb=" N GLU a 263 " --> pdb=" O ASP a 260 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA a 264 " --> pdb=" O ALA a 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 260 through 264' Processing helix chain 'a' and resid 265 through 273 Processing helix chain 'a' and resid 279 through 293 Proline residue: a 290 - end of helix Processing helix chain 'a' and resid 295 through 317 removed outlier: 4.139A pdb=" N VAL a 299 " --> pdb=" O SER a 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 322 through 348 removed outlier: 3.581A pdb=" N ILE a 326 " --> pdb=" O ASP a 322 " (cutoff:3.500A) Processing helix chain 'a' and resid 352 through 356 removed outlier: 3.871A pdb=" N GLY a 355 " --> pdb=" O ASP a 352 " (cutoff:3.500A) Processing helix chain 'a' and resid 359 through 392 removed outlier: 3.852A pdb=" N VAL a 363 " --> pdb=" O PHE a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 406 through 422 removed outlier: 3.657A pdb=" N GLY a 422 " --> pdb=" O LEU a 418 " (cutoff:3.500A) Processing helix chain 'a' and resid 427 through 441 removed outlier: 3.508A pdb=" N SER a 431 " --> pdb=" O ASN a 427 " (cutoff:3.500A) Processing helix chain 'a' and resid 447 through 449 No H-bonds generated for 'chain 'a' and resid 447 through 449' Processing helix chain 'a' and resid 450 through 473 removed outlier: 4.644A pdb=" N VAL a 454 " --> pdb=" O VAL a 450 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL a 455 " --> pdb=" O ILE a 451 " (cutoff:3.500A) Processing helix chain 'a' and resid 492 through 512 removed outlier: 3.601A pdb=" N LEU a 496 " --> pdb=" O PRO a 492 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA a 498 " --> pdb=" O GLY a 494 " (cutoff:3.500A) Proline residue: a 499 - end of helix Processing helix chain 'a' and resid 513 through 520 removed outlier: 3.576A pdb=" N SER a 517 " --> pdb=" O PRO a 513 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 529 removed outlier: 3.610A pdb=" N ALA a 524 " --> pdb=" O VAL a 520 " (cutoff:3.500A) Processing helix chain 'a' and resid 536 through 544 removed outlier: 3.671A pdb=" N ASP a 540 " --> pdb=" O ASN a 536 " (cutoff:3.500A) Processing helix chain 'a' and resid 551 through 568 removed outlier: 3.838A pdb=" N MET a 555 " --> pdb=" O PRO a 551 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG a 568 " --> pdb=" O LEU a 564 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 584 removed outlier: 3.834A pdb=" N MET a 584 " --> pdb=" O LEU a 580 " (cutoff:3.500A) Processing helix chain 'a' and resid 586 through 609 Processing helix chain 'a' and resid 612 through 635 removed outlier: 3.645A pdb=" N TYR a 616 " --> pdb=" O SER a 612 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS a 635 " --> pdb=" O THR a 631 " (cutoff:3.500A) Processing helix chain 'a' and resid 649 through 668 Processing helix chain 'a' and resid 671 through 693 removed outlier: 3.792A pdb=" N ALA a 675 " --> pdb=" O SER a 671 " (cutoff:3.500A) Processing helix chain 'a' and resid 695 through 718 removed outlier: 3.573A pdb=" N TYR a 718 " --> pdb=" O LEU a 714 " (cutoff:3.500A) Processing helix chain 'a' and resid 733 through 756 Processing helix chain 'a' and resid 764 through 770 Processing helix chain 'a' and resid 780 through 787 Processing helix chain 'a' and resid 790 through 813 removed outlier: 3.598A pdb=" N LEU a 794 " --> pdb=" O GLY a 790 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE a 795 " --> pdb=" O PHE a 791 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 29 Proline residue: b 17 - end of helix Processing helix chain 'b' and resid 36 through 55 Processing helix chain 'b' and resid 57 through 64 removed outlier: 3.715A pdb=" N ARG b 61 " --> pdb=" O ILE b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 89 removed outlier: 3.834A pdb=" N LEU b 71 " --> pdb=" O ASN b 67 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU b 89 " --> pdb=" O SER b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 138 removed outlier: 3.513A pdb=" N PHE b 117 " --> pdb=" O THR b 113 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU b 138 " --> pdb=" O GLU b 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 21 Processing helix chain 'c' and resid 24 through 48 removed outlier: 3.529A pdb=" N ILE c 28 " --> pdb=" O SER c 24 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY c 48 " --> pdb=" O LEU c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 66 through 98 removed outlier: 4.529A pdb=" N GLN c 70 " --> pdb=" O ASP c 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 1 through 5 removed outlier: 4.209A pdb=" N LEU d 5 " --> pdb=" O SER d 2 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 19 Proline residue: d 12 - end of helix Processing helix chain 'd' and resid 25 through 54 Processing helix chain 'd' and resid 75 through 100 Processing helix chain 'd' and resid 101 through 107 removed outlier: 3.661A pdb=" N GLU d 105 " --> pdb=" O GLY d 101 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE d 107 " --> pdb=" O LYS d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 125 Processing helix chain 'd' and resid 128 through 149 Processing helix chain 'd' and resid 152 through 184 Processing helix chain 'd' and resid 188 through 199 Processing helix chain 'd' and resid 202 through 220 removed outlier: 3.997A pdb=" N THR d 206 " --> pdb=" O SER d 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 228 through 235 Processing helix chain 'd' and resid 237 through 263 removed outlier: 5.409A pdb=" N THR d 249 " --> pdb=" O GLY d 245 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS d 250 " --> pdb=" O GLY d 246 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL d 251 " --> pdb=" O LEU d 247 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY d 252 " --> pdb=" O LEU d 248 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL d 253 " --> pdb=" O THR d 249 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 293 removed outlier: 4.435A pdb=" N THR d 271 " --> pdb=" O ASP d 267 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR d 293 " --> pdb=" O GLY d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 295 through 316 Processing helix chain 'd' and resid 319 through 352 Processing helix chain 'd' and resid 355 through 359 removed outlier: 3.763A pdb=" N PHE d 359 " --> pdb=" O ILE d 356 " (cutoff:3.500A) Processing helix chain 'd' and resid 366 through 382 Processing helix chain 'd' and resid 386 through 388 No H-bonds generated for 'chain 'd' and resid 386 through 388' Processing helix chain 'd' and resid 389 through 402 Processing helix chain 'd' and resid 404 through 430 removed outlier: 3.560A pdb=" N ALA d 408 " --> pdb=" O LEU d 404 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 462 removed outlier: 4.150A pdb=" N VAL d 449 " --> pdb=" O ARG d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 462 through 478 Proline residue: d 468 - end of helix Processing helix chain 'd' and resid 480 through 488 removed outlier: 3.613A pdb=" N LEU d 488 " --> pdb=" O ILE d 484 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 19 removed outlier: 3.609A pdb=" N THR e 19 " --> pdb=" O TRP e 15 " (cutoff:3.500A) Processing helix chain 'e' and resid 23 through 41 Processing helix chain 'e' and resid 50 through 80 removed outlier: 3.680A pdb=" N VAL e 54 " --> pdb=" O TYR e 50 " (cutoff:3.500A) Processing helix chain 'e' and resid 99 through 112 removed outlier: 3.723A pdb=" N LEU e 112 " --> pdb=" O MET e 108 " (cutoff:3.500A) Processing helix chain 'e' and resid 140 through 157 removed outlier: 3.643A pdb=" N SER e 157 " --> pdb=" O ILE e 153 " (cutoff:3.500A) Processing helix chain 'f' and resid 3 through 23 Processing helix chain 'f' and resid 26 through 53 removed outlier: 4.329A pdb=" N ARG f 30 " --> pdb=" O SER f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 57 through 80 removed outlier: 3.585A pdb=" N ILE f 61 " --> pdb=" O PHE f 57 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU f 80 " --> pdb=" O ALA f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 34 Processing helix chain 'g' and resid 36 through 67 removed outlier: 3.562A pdb=" N ASN g 67 " --> pdb=" O PHE g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 71 through 99 removed outlier: 4.207A pdb=" N LEU g 75 " --> pdb=" O ASN g 71 " (cutoff:3.500A) Proline residue: g 86 - end of helix removed outlier: 3.502A pdb=" N ALA g 99 " --> pdb=" O ALA g 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 92 removed outlier: 6.969A pdb=" N ILE A 97 " --> pdb=" O TRP A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 101 Processing sheet with id=AA3, first strand: chain 'D' and resid 57 through 60 Processing sheet with id=AA4, first strand: chain 'E' and resid 89 through 94 removed outlier: 7.440A pdb=" N THR E 127 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N VAL E 121 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR E 129 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU E 119 " --> pdb=" O TYR E 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 85 through 92 removed outlier: 7.014A pdb=" N ILE a 97 " --> pdb=" O TRP a 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 98 through 101 Processing sheet with id=AA7, first strand: chain 'd' and resid 57 through 60 Processing sheet with id=AA8, first strand: chain 'e' and resid 89 through 94 removed outlier: 7.448A pdb=" N THR e 127 " --> pdb=" O VAL e 121 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL e 121 " --> pdb=" O THR e 127 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR e 129 " --> pdb=" O LEU e 119 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU e 119 " --> pdb=" O TYR e 129 " (cutoff:3.500A) 2167 hydrogen bonds defined for protein. 6459 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: 5.11 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4572 1.32 - 1.45: 8315 1.45 - 1.57: 17759 1.57 - 1.69: 46 1.69 - 1.82: 270 Bond restraints: 30962 Sorted by residual: bond pdb=" O14 PTY B 201 " pdb=" P1 PTY B 201 " ideal model delta sigma weight residual 1.646 1.462 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" O14 PTY E 201 " pdb=" P1 PTY E 201 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.13e+01 bond pdb=" O14 PTY a 906 " pdb=" P1 PTY a 906 " ideal model delta sigma weight residual 1.646 1.466 0.180 2.00e-02 2.50e+03 8.12e+01 bond pdb=" O14 PTY A 906 " pdb=" P1 PTY A 906 " ideal model delta sigma weight residual 1.646 1.470 0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" O14 PTY a 902 " pdb=" P1 PTY a 902 " ideal model delta sigma weight residual 1.646 1.470 0.176 2.00e-02 2.50e+03 7.73e+01 ... (remaining 30957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 40913 3.06 - 6.13: 841 6.13 - 9.19: 144 9.19 - 12.25: 40 12.25 - 15.32: 4 Bond angle restraints: 41942 Sorted by residual: angle pdb=" N PRO D 384 " pdb=" CA PRO D 384 " pdb=" C PRO D 384 " ideal model delta sigma weight residual 110.70 117.69 -6.99 1.22e+00 6.72e-01 3.28e+01 angle pdb=" N PRO d 384 " pdb=" CA PRO d 384 " pdb=" C PRO d 384 " ideal model delta sigma weight residual 110.70 117.34 -6.64 1.22e+00 6.72e-01 2.96e+01 angle pdb=" C ASN a 81 " pdb=" N ASP a 82 " pdb=" CA ASP a 82 " ideal model delta sigma weight residual 121.54 131.02 -9.48 1.91e+00 2.74e-01 2.46e+01 angle pdb=" C VAL G 108 " pdb=" N ARG G 109 " pdb=" CA ARG G 109 " ideal model delta sigma weight residual 121.31 128.61 -7.30 1.49e+00 4.50e-01 2.40e+01 angle pdb=" N ALA D 235 " pdb=" CA ALA D 235 " pdb=" C ALA D 235 " ideal model delta sigma weight residual 112.17 118.78 -6.61 1.36e+00 5.41e-01 2.36e+01 ... (remaining 41937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 17721 34.92 - 69.84: 156 69.84 - 104.77: 32 104.77 - 139.69: 10 139.69 - 174.61: 5 Dihedral angle restraints: 17924 sinusoidal: 7084 harmonic: 10840 Sorted by residual: dihedral pdb=" CA ASP E 120 " pdb=" C ASP E 120 " pdb=" N VAL E 121 " pdb=" CA VAL E 121 " ideal model delta harmonic sigma weight residual 180.00 148.77 31.23 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ASP e 120 " pdb=" C ASP e 120 " pdb=" N VAL e 121 " pdb=" CA VAL e 121 " ideal model delta harmonic sigma weight residual 180.00 150.83 29.17 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA PHE e 49 " pdb=" C PHE e 49 " pdb=" N TYR e 50 " pdb=" CA TYR e 50 " ideal model delta harmonic sigma weight residual -180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 17921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4100 0.074 - 0.147: 762 0.147 - 0.221: 108 0.221 - 0.295: 10 0.295 - 0.369: 8 Chirality restraints: 4988 Sorted by residual: chirality pdb=" C6 PTY A 906 " pdb=" C1 PTY A 906 " pdb=" C5 PTY A 906 " pdb=" O7 PTY A 906 " both_signs ideal model delta sigma weight residual False 2.49 2.12 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" C6 PTY B 201 " pdb=" C1 PTY B 201 " pdb=" C5 PTY B 201 " pdb=" O7 PTY B 201 " both_signs ideal model delta sigma weight residual False 2.49 2.13 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C6 PTY a 907 " pdb=" C1 PTY a 907 " pdb=" C5 PTY a 907 " pdb=" O7 PTY a 907 " both_signs ideal model delta sigma weight residual False 2.49 2.13 0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 4985 not shown) Planarity restraints: 4948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 374 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C ALA A 374 " -0.088 2.00e-02 2.50e+03 pdb=" O ALA A 374 " 0.033 2.00e-02 2.50e+03 pdb=" N THR A 375 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA a 374 " -0.025 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C ALA a 374 " 0.086 2.00e-02 2.50e+03 pdb=" O ALA a 374 " -0.033 2.00e-02 2.50e+03 pdb=" N THR a 375 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 373 " -0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C HIS A 373 " 0.073 2.00e-02 2.50e+03 pdb=" O HIS A 373 " -0.028 2.00e-02 2.50e+03 pdb=" N ALA A 374 " -0.025 2.00e-02 2.50e+03 ... (remaining 4945 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 8453 2.82 - 3.40: 33251 3.40 - 3.98: 57430 3.98 - 4.56: 80976 4.56 - 5.14: 121675 Nonbonded interactions: 301785 Sorted by model distance: nonbonded pdb=" O TYR A 767 " pdb=" OG1 THR A 771 " model vdw 2.238 3.040 nonbonded pdb=" O GLN d 155 " pdb=" OG1 THR d 159 " model vdw 2.242 3.040 nonbonded pdb=" O GLN D 155 " pdb=" OG1 THR D 159 " model vdw 2.243 3.040 nonbonded pdb=" O TYR a 767 " pdb=" OG1 THR a 771 " model vdw 2.249 3.040 nonbonded pdb=" O PHE A 315 " pdb=" OH TYR A 577 " model vdw 2.261 3.040 ... (remaining 301780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'a' } ncs_group { reference = (chain 'B' and resid 3 through 140) selection = chain 'b' } ncs_group { reference = chain 'C' selection = chain 'c' } ncs_group { reference = chain 'D' selection = chain 'd' } ncs_group { reference = (chain 'E' and resid 1 through 158) selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 26.060 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 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 0.184 30962 Z= 0.375 Angle : 1.135 15.316 41942 Z= 0.579 Chirality : 0.060 0.369 4988 Planarity : 0.009 0.063 4948 Dihedral : 12.510 174.609 10964 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.10 % Allowed : 2.74 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.64 (0.11), residues: 3716 helix: -1.12 (0.08), residues: 2742 sheet: -1.47 (0.57), residues: 70 loop : -3.36 (0.16), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 473 TYR 0.040 0.003 TYR A 619 PHE 0.047 0.004 PHE c 87 TRP 0.030 0.004 TRP a 166 HIS 0.013 0.002 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.37 (30962) covalent geometry : angle 1.13469 / 0.58 (41942) hydrogen bonds : bond 0.14082 / 9.21 ( 2167) hydrogen bonds : angle 5.79949 / 4.18 ( 6459) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 773 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7753 (t0) cc_final: 0.7550 (t0) REVERT: A 131 LYS cc_start: 0.6419 (ttpp) cc_final: 0.5842 (tttt) REVERT: A 319 LYS cc_start: 0.8005 (tmtm) cc_final: 0.7766 (tptp) REVERT: A 357 ASN cc_start: 0.5945 (t0) cc_final: 0.5734 (p0) REVERT: A 372 ASN cc_start: 0.8244 (t0) cc_final: 0.7993 (t0) REVERT: A 440 LEU cc_start: 0.7946 (mt) cc_final: 0.7280 (tm) REVERT: A 514 ASN cc_start: 0.7088 (m-40) cc_final: 0.6580 (p0) REVERT: A 568 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.6840 (mpt-90) REVERT: C 60 LYS cc_start: 0.7381 (mttt) cc_final: 0.6699 (ttpp) REVERT: C 63 ARG cc_start: 0.8979 (ptm160) cc_final: 0.8519 (ptm-80) REVERT: D 293 TYR cc_start: 0.8076 (m-80) cc_final: 0.7809 (m-80) REVERT: D 318 MET cc_start: 0.6703 (mmp) cc_final: 0.5449 (pmt) REVERT: E 102 GLU cc_start: 0.7866 (pt0) cc_final: 0.6156 (mp0) REVERT: E 126 SER cc_start: 0.6689 (p) cc_final: 0.6384 (p) REVERT: F 86 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7198 (mm-30) REVERT: G 100 ASN cc_start: 0.7430 (m-40) cc_final: 0.6924 (t0) REVERT: a 48 PHE cc_start: 0.7566 (t80) cc_final: 0.7358 (t80) REVERT: a 89 MET cc_start: 0.7482 (ttm) cc_final: 0.7248 (ttm) REVERT: a 514 ASN cc_start: 0.7425 (m-40) cc_final: 0.7073 (m110) REVERT: a 568 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7020 (mpt-90) REVERT: c 60 LYS cc_start: 0.7501 (mttt) cc_final: 0.7051 (ttpp) REVERT: c 63 ARG cc_start: 0.9081 (ptm160) cc_final: 0.8649 (ptm-80) REVERT: d 113 PHE cc_start: 0.8675 (t80) cc_final: 0.8416 (t80) REVERT: d 197 ASN cc_start: 0.8528 (m-40) cc_final: 0.8149 (t0) REVERT: e 77 LYS cc_start: 0.7547 (pttm) cc_final: 0.7279 (mttm) REVERT: e 83 SER cc_start: 0.7017 (m) cc_final: 0.6679 (t) REVERT: e 99 LYS cc_start: 0.8159 (ptpt) cc_final: 0.7819 (ptmt) REVERT: e 102 GLU cc_start: 0.7868 (pt0) cc_final: 0.6143 (mp0) REVERT: e 126 SER cc_start: 0.6744 (p) cc_final: 0.6524 (p) REVERT: f 86 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7220 (mm-30) REVERT: g 94 ARG cc_start: 0.7600 (ttp-110) cc_final: 0.7229 (ttp80) REVERT: g 100 ASN cc_start: 0.7833 (m-40) cc_final: 0.7278 (t0) outliers start: 3 outliers final: 1 residues processed: 776 average time/residue: 0.5324 time to fit residues: 505.4212 Evaluate side-chains 491 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 490 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 153 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 HIS A 320 GLN A 733 HIS A 736 ASN C 102 HIS D 266 HIS ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS a 158 HIS a 191 GLN a 610 ASN a 733 HIS ** a 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.116128 restraints weight = 43305.071| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.86 r_work: 0.3323 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 30962 Z= 0.231 Angle : 0.750 11.245 41942 Z= 0.387 Chirality : 0.047 0.237 4988 Planarity : 0.006 0.056 4948 Dihedral : 12.713 172.821 4652 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.45 % Allowed : 10.94 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.23 (0.13), residues: 3716 helix: 0.75 (0.09), residues: 2770 sheet: -0.54 (0.55), residues: 90 loop : -3.07 (0.17), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 644 TYR 0.030 0.002 TYR a 466 PHE 0.032 0.002 PHE A 376 TRP 0.017 0.002 TRP D 371 HIS 0.010 0.002 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (30962) covalent geometry : angle 0.74961 / 0.39 (41942) hydrogen bonds : bond 0.07097 / 4.63 ( 2167) hydrogen bonds : angle 4.43314 / 3.19 ( 6459) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 534 time to evaluate : 1.161 Fit side-chains REVERT: A 131 LYS cc_start: 0.6409 (ttpp) cc_final: 0.5945 (tttt) REVERT: A 351 TYR cc_start: 0.7405 (t80) cc_final: 0.7110 (t80) REVERT: A 372 ASN cc_start: 0.8481 (t0) cc_final: 0.8183 (t0) REVERT: A 440 LEU cc_start: 0.8049 (mt) cc_final: 0.7270 (tm) REVERT: A 568 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.6839 (mpt-90) REVERT: A 701 THR cc_start: 0.8578 (p) cc_final: 0.8122 (m) REVERT: A 722 LYS cc_start: 0.8030 (mmpt) cc_final: 0.7093 (mmtm) REVERT: B 78 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6867 (t80) REVERT: C 60 LYS cc_start: 0.7288 (mttt) cc_final: 0.6822 (ttpp) REVERT: C 63 ARG cc_start: 0.8843 (ptm160) cc_final: 0.8389 (ptm-80) REVERT: D 293 TYR cc_start: 0.8299 (m-80) cc_final: 0.8068 (m-80) REVERT: D 318 MET cc_start: 0.6963 (mmp) cc_final: 0.5794 (pmt) REVERT: E 110 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7318 (pt) REVERT: E 157 SER cc_start: 0.6852 (t) cc_final: 0.6561 (m) REVERT: F 58 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7944 (mt) REVERT: F 86 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7349 (mm-30) REVERT: a 48 PHE cc_start: 0.6967 (t80) cc_final: 0.6652 (t80) REVERT: a 440 LEU cc_start: 0.8216 (mm) cc_final: 0.7541 (tm) REVERT: a 568 ARG cc_start: 0.8147 (tpp-160) cc_final: 0.7027 (mpt-90) REVERT: b 78 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.7191 (t80) REVERT: c 60 LYS cc_start: 0.7376 (mttt) cc_final: 0.7059 (ttpp) REVERT: c 63 ARG cc_start: 0.8791 (ptm160) cc_final: 0.8395 (ptm-80) REVERT: d 5 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8062 (tt) REVERT: d 137 GLU cc_start: 0.7947 (mp0) cc_final: 0.7633 (mp0) REVERT: d 197 ASN cc_start: 0.8481 (m-40) cc_final: 0.8264 (t0) REVERT: d 446 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8237 (tt) REVERT: e 99 LYS cc_start: 0.8140 (ptpt) cc_final: 0.7937 (ptmt) REVERT: e 102 GLU cc_start: 0.7709 (pt0) cc_final: 0.7138 (pt0) REVERT: e 108 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8085 (tmm) REVERT: f 86 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7385 (mm-30) REVERT: g 94 ARG cc_start: 0.7512 (ttp-110) cc_final: 0.7216 (ttm170) REVERT: g 100 ASN cc_start: 0.7786 (m-40) cc_final: 0.7355 (t0) outliers start: 108 outliers final: 41 residues processed: 591 average time/residue: 0.5135 time to fit residues: 374.5015 Evaluate side-chains 525 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 477 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 746 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 396 ILE Chi-restraints excluded: chain a residue 455 VAL Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 792 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain c residue 62 SER Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 318 MET Chi-restraints excluded: chain d residue 446 LEU Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain d residue 489 LYS Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 90 ILE Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 265 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 150 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 239 optimal weight: 8.9990 chunk 274 optimal weight: 5.9990 chunk 292 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 GLN a 610 ASN d 3 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 10 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.145894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119887 restraints weight = 42808.554| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.79 r_work: 0.3393 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30962 Z= 0.158 Angle : 0.652 11.254 41942 Z= 0.336 Chirality : 0.043 0.339 4988 Planarity : 0.005 0.055 4948 Dihedral : 12.035 161.802 4652 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.64 % Allowed : 13.15 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 0.64 (0.14), residues: 3716 helix: 1.43 (0.10), residues: 2756 sheet: -0.21 (0.58), residues: 90 loop : -2.90 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 394 TYR 0.028 0.002 TYR a 466 PHE 0.035 0.002 PHE A 376 TRP 0.013 0.001 TRP A 298 HIS 0.006 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (30962) covalent geometry : angle 0.65244 / 0.34 (41942) hydrogen bonds : bond 0.05967 / 3.88 ( 2167) hydrogen bonds : angle 4.14437 / 2.98 ( 6459) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 557 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8240 (m) cc_final: 0.7740 (p) REVERT: A 123 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8885 (tm) REVERT: A 131 LYS cc_start: 0.6429 (ttpp) cc_final: 0.5964 (tttt) REVERT: A 351 TYR cc_start: 0.7457 (t80) cc_final: 0.7052 (t80) REVERT: A 354 MET cc_start: 0.6625 (pmm) cc_final: 0.6216 (tpp) REVERT: A 372 ASN cc_start: 0.8397 (t0) cc_final: 0.8079 (m110) REVERT: A 440 LEU cc_start: 0.7944 (mt) cc_final: 0.7572 (tm) REVERT: A 568 ARG cc_start: 0.8051 (tpp-160) cc_final: 0.6823 (mpt-90) REVERT: A 688 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 701 THR cc_start: 0.8565 (p) cc_final: 0.8160 (m) REVERT: A 722 LYS cc_start: 0.7976 (mmpt) cc_final: 0.7092 (mmtm) REVERT: B 78 PHE cc_start: 0.7183 (OUTLIER) cc_final: 0.6854 (t80) REVERT: C 60 LYS cc_start: 0.7044 (mttt) cc_final: 0.6704 (ttpp) REVERT: C 63 ARG cc_start: 0.8805 (ptm160) cc_final: 0.8363 (ptm-80) REVERT: D 5 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7836 (tt) REVERT: D 229 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8015 (tt) REVERT: D 293 TYR cc_start: 0.8217 (m-80) cc_final: 0.7928 (m-80) REVERT: D 318 MET cc_start: 0.6893 (mmp) cc_final: 0.5799 (pmm) REVERT: E 110 ILE cc_start: 0.7880 (OUTLIER) cc_final: 0.7423 (pt) REVERT: E 157 SER cc_start: 0.6955 (t) cc_final: 0.6633 (m) REVERT: a 48 PHE cc_start: 0.6889 (t80) cc_final: 0.6584 (t80) REVERT: a 78 ASP cc_start: 0.7607 (t0) cc_final: 0.7335 (t0) REVERT: a 440 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7502 (tm) REVERT: a 472 SER cc_start: 0.8951 (t) cc_final: 0.8671 (m) REVERT: a 568 ARG cc_start: 0.8137 (tpp-160) cc_final: 0.7010 (mpt-90) REVERT: a 651 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: a 701 THR cc_start: 0.8725 (p) cc_final: 0.8406 (m) REVERT: c 60 LYS cc_start: 0.7106 (mttt) cc_final: 0.6882 (ttpp) REVERT: c 63 ARG cc_start: 0.8743 (ptm160) cc_final: 0.8351 (ptm-80) REVERT: d 5 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7914 (tt) REVERT: d 405 ILE cc_start: 0.8616 (mm) cc_final: 0.8321 (mt) REVERT: e 108 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8051 (tmm) REVERT: e 110 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7361 (pt) REVERT: f 86 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7461 (mm-30) REVERT: g 71 ASN cc_start: 0.8599 (m110) cc_final: 0.8193 (m-40) REVERT: g 94 ARG cc_start: 0.7407 (ttp-110) cc_final: 0.7155 (ttm170) REVERT: g 100 ASN cc_start: 0.7728 (m-40) cc_final: 0.7334 (t0) outliers start: 114 outliers final: 32 residues processed: 603 average time/residue: 0.4882 time to fit residues: 365.1308 Evaluate side-chains 531 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 488 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 651 TYR Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain c residue 62 SER Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 318 MET Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain g residue 13 VAL Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 151 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 346 optimal weight: 8.9990 chunk 211 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 3 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN a 191 GLN a 372 ASN ** a 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.144626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118547 restraints weight = 42725.639| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.78 r_work: 0.3374 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30962 Z= 0.176 Angle : 0.673 14.143 41942 Z= 0.343 Chirality : 0.044 0.355 4988 Planarity : 0.005 0.057 4948 Dihedral : 11.756 168.386 4652 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.70 % Allowed : 13.91 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.14), residues: 3716 helix: 1.64 (0.10), residues: 2740 sheet: -0.37 (0.57), residues: 94 loop : -2.80 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 649 TYR 0.024 0.002 TYR a 466 PHE 0.033 0.002 PHE A 376 TRP 0.012 0.001 TRP a 298 HIS 0.008 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (30962) covalent geometry : angle 0.67288 / 0.34 (41942) hydrogen bonds : bond 0.06026 / 3.92 ( 2167) hydrogen bonds : angle 4.11410 / 2.96 ( 6459) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 522 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8192 (m) cc_final: 0.7667 (p) REVERT: A 123 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8897 (tm) REVERT: A 131 LYS cc_start: 0.6433 (ttpp) cc_final: 0.5970 (tttt) REVERT: A 354 MET cc_start: 0.6771 (pmm) cc_final: 0.6455 (tpp) REVERT: A 371 PHE cc_start: 0.8541 (t80) cc_final: 0.8252 (t80) REVERT: A 440 LEU cc_start: 0.7866 (mt) cc_final: 0.7536 (tm) REVERT: A 568 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.6829 (mpt-90) REVERT: A 688 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8645 (tt) REVERT: A 701 THR cc_start: 0.8551 (p) cc_final: 0.8195 (m) REVERT: A 722 LYS cc_start: 0.7998 (mmpt) cc_final: 0.7117 (mmtm) REVERT: B 134 GLU cc_start: 0.7625 (pt0) cc_final: 0.7397 (tt0) REVERT: C 60 LYS cc_start: 0.7019 (mttt) cc_final: 0.6667 (ttpp) REVERT: C 63 ARG cc_start: 0.8761 (ptm160) cc_final: 0.8334 (ptm-80) REVERT: D 5 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7887 (tt) REVERT: D 229 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8014 (tt) REVERT: D 293 TYR cc_start: 0.8227 (m-80) cc_final: 0.7950 (m-80) REVERT: E 64 PHE cc_start: 0.6926 (m-10) cc_final: 0.6690 (m-10) REVERT: E 108 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.7801 (tmm) REVERT: E 110 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7360 (pt) REVERT: E 157 SER cc_start: 0.7028 (t) cc_final: 0.6678 (m) REVERT: a 48 PHE cc_start: 0.6900 (t80) cc_final: 0.6572 (t80) REVERT: a 439 MET cc_start: 0.7922 (mtp) cc_final: 0.7711 (ptm) REVERT: a 440 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7628 (tm) REVERT: a 568 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7017 (mpt-90) REVERT: a 701 THR cc_start: 0.8735 (p) cc_final: 0.8468 (m) REVERT: a 722 LYS cc_start: 0.8192 (mmpt) cc_final: 0.7245 (mmtm) REVERT: b 62 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8166 (ttpp) REVERT: b 78 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7357 (t80) REVERT: c 63 ARG cc_start: 0.8736 (ptm160) cc_final: 0.8348 (ptm-80) REVERT: d 5 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7948 (tt) REVERT: d 109 TYR cc_start: 0.7821 (t80) cc_final: 0.7589 (t80) REVERT: d 293 TYR cc_start: 0.8183 (m-80) cc_final: 0.7980 (m-80) REVERT: d 405 ILE cc_start: 0.8612 (mm) cc_final: 0.8380 (mt) REVERT: e 102 GLU cc_start: 0.7502 (pt0) cc_final: 0.7299 (pt0) REVERT: e 108 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8074 (tmm) REVERT: e 110 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7505 (pt) REVERT: f 86 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7440 (mm-30) REVERT: g 71 ASN cc_start: 0.8627 (m110) cc_final: 0.8208 (m-40) REVERT: g 94 ARG cc_start: 0.7421 (ttp-110) cc_final: 0.7177 (ttm170) REVERT: g 100 ASN cc_start: 0.7757 (m-40) cc_final: 0.7324 (t0) outliers start: 116 outliers final: 47 residues processed: 579 average time/residue: 0.5144 time to fit residues: 368.0968 Evaluate side-chains 535 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 476 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 455 VAL Chi-restraints excluded: chain a residue 610 ASN Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 62 LYS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 77 LYS Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 323 optimal weight: 0.0020 chunk 90 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 360 optimal weight: 30.0000 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 96 HIS ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.119617 restraints weight = 43084.917| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.89 r_work: 0.3378 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30962 Z= 0.134 Angle : 0.619 12.590 41942 Z= 0.314 Chirality : 0.042 0.353 4988 Planarity : 0.004 0.054 4948 Dihedral : 11.123 177.436 4652 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.38 % Allowed : 14.90 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.14), residues: 3716 helix: 1.87 (0.10), residues: 2766 sheet: -0.14 (0.59), residues: 94 loop : -2.74 (0.18), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 394 TYR 0.027 0.001 TYR a 466 PHE 0.034 0.001 PHE A 376 TRP 0.012 0.001 TRP a 298 HIS 0.004 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (30962) covalent geometry : angle 0.61900 / 0.31 (41942) hydrogen bonds : bond 0.05197 / 3.38 ( 2167) hydrogen bonds : angle 3.93756 / 2.83 ( 6459) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 547 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.7999 (m) cc_final: 0.7440 (p) REVERT: A 123 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8857 (tm) REVERT: A 131 LYS cc_start: 0.6424 (ttpp) cc_final: 0.5946 (tttt) REVERT: A 371 PHE cc_start: 0.8508 (t80) cc_final: 0.8255 (t80) REVERT: A 440 LEU cc_start: 0.7915 (mt) cc_final: 0.7616 (tm) REVERT: A 568 ARG cc_start: 0.8002 (tpp-160) cc_final: 0.6754 (mpt-90) REVERT: A 688 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8480 (tt) REVERT: A 701 THR cc_start: 0.8655 (p) cc_final: 0.8277 (m) REVERT: B 18 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8131 (tp) REVERT: C 23 LYS cc_start: 0.7144 (tttt) cc_final: 0.6304 (tmmt) REVERT: C 24 SER cc_start: 0.6217 (OUTLIER) cc_final: 0.5957 (m) REVERT: C 60 LYS cc_start: 0.6997 (mttt) cc_final: 0.6542 (ttpp) REVERT: C 63 ARG cc_start: 0.8669 (ptm160) cc_final: 0.8209 (ptm-80) REVERT: D 5 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8028 (tt) REVERT: D 189 MET cc_start: 0.8427 (mtt) cc_final: 0.8219 (mtt) REVERT: D 197 ASN cc_start: 0.8394 (m-40) cc_final: 0.8011 (t0) REVERT: D 293 TYR cc_start: 0.8185 (m-80) cc_final: 0.7901 (m-80) REVERT: E 64 PHE cc_start: 0.6954 (m-10) cc_final: 0.6669 (m-10) REVERT: E 102 GLU cc_start: 0.7179 (pt0) cc_final: 0.6740 (pt0) REVERT: E 108 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7759 (tmm) REVERT: E 110 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7244 (pt) REVERT: F 37 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7802 (mtp) REVERT: F 58 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7443 (mt) REVERT: G 94 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7252 (ttp80) REVERT: a 48 PHE cc_start: 0.6868 (t80) cc_final: 0.6502 (t80) REVERT: a 440 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7663 (tm) REVERT: a 568 ARG cc_start: 0.8104 (tpp-160) cc_final: 0.6909 (mpt-90) REVERT: a 701 THR cc_start: 0.8681 (p) cc_final: 0.8473 (m) REVERT: a 722 LYS cc_start: 0.8228 (mmpt) cc_final: 0.7251 (mmtm) REVERT: b 78 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7380 (t80) REVERT: b 100 TYR cc_start: 0.7498 (m-80) cc_final: 0.7278 (m-80) REVERT: c 63 ARG cc_start: 0.8661 (ptm160) cc_final: 0.8228 (ptm-80) REVERT: d 293 TYR cc_start: 0.8181 (m-80) cc_final: 0.7938 (m-80) REVERT: e 102 GLU cc_start: 0.7486 (pt0) cc_final: 0.7217 (pt0) REVERT: e 108 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8095 (tmm) REVERT: e 110 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7363 (pt) REVERT: f 86 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7354 (mm-30) REVERT: g 64 PHE cc_start: 0.8692 (t80) cc_final: 0.7828 (t80) REVERT: g 71 ASN cc_start: 0.8649 (m110) cc_final: 0.8218 (m-40) REVERT: g 94 ARG cc_start: 0.7409 (ttp-110) cc_final: 0.7128 (ttp80) REVERT: g 100 ASN cc_start: 0.7738 (m-40) cc_final: 0.7248 (t0) outliers start: 106 outliers final: 33 residues processed: 605 average time/residue: 0.4990 time to fit residues: 376.6198 Evaluate side-chains 537 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 491 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain a residue 792 ASP Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 153 ILE Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 363 optimal weight: 10.0000 chunk 211 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 341 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 217 optimal weight: 5.9990 chunk 227 optimal weight: 0.0570 chunk 312 optimal weight: 9.9990 chunk 37 optimal weight: 0.0670 overall best weight: 4.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 303 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN a 702 GLN c 96 GLN d 303 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117344 restraints weight = 43245.347| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.92 r_work: 0.3340 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30962 Z= 0.179 Angle : 0.674 11.304 41942 Z= 0.340 Chirality : 0.044 0.361 4988 Planarity : 0.005 0.054 4948 Dihedral : 11.172 179.805 4652 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.51 % Allowed : 16.21 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.22 (0.14), residues: 3716 helix: 1.85 (0.10), residues: 2764 sheet: -0.12 (0.58), residues: 94 loop : -2.69 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 394 TYR 0.021 0.002 TYR A 466 PHE 0.030 0.002 PHE A 376 TRP 0.011 0.001 TRP a 298 HIS 0.009 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (30962) covalent geometry : angle 0.67416 / 0.34 (41942) hydrogen bonds : bond 0.05789 / 3.78 ( 2167) hydrogen bonds : angle 4.03225 / 2.90 ( 6459) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 501 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8121 (m) cc_final: 0.7562 (p) REVERT: A 123 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8800 (tm) REVERT: A 131 LYS cc_start: 0.6351 (ttpp) cc_final: 0.5885 (tttt) REVERT: A 277 MET cc_start: 0.7813 (tpt) cc_final: 0.7005 (tpt) REVERT: A 440 LEU cc_start: 0.7856 (mt) cc_final: 0.7620 (tm) REVERT: A 568 ARG cc_start: 0.8000 (tpp-160) cc_final: 0.6713 (mpt-90) REVERT: A 688 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8593 (tt) REVERT: A 701 THR cc_start: 0.8607 (p) cc_final: 0.8252 (m) REVERT: A 722 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7077 (mmtm) REVERT: B 18 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8218 (tp) REVERT: C 23 LYS cc_start: 0.7168 (tttt) cc_final: 0.6288 (tmmt) REVERT: C 60 LYS cc_start: 0.7131 (mttt) cc_final: 0.6606 (ttpp) REVERT: C 63 ARG cc_start: 0.8653 (ptm160) cc_final: 0.8183 (ptm-80) REVERT: D 5 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7936 (tt) REVERT: D 137 GLU cc_start: 0.7715 (mp0) cc_final: 0.7300 (mp0) REVERT: D 229 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7959 (tt) REVERT: D 293 TYR cc_start: 0.8197 (m-80) cc_final: 0.7903 (m-80) REVERT: D 461 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8445 (mp) REVERT: E 64 PHE cc_start: 0.6948 (m-10) cc_final: 0.6714 (m-10) REVERT: E 108 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7743 (tmm) REVERT: E 110 ILE cc_start: 0.7611 (OUTLIER) cc_final: 0.7207 (pt) REVERT: E 119 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7704 (pp) REVERT: E 157 SER cc_start: 0.6947 (t) cc_final: 0.6593 (m) REVERT: G 94 ARG cc_start: 0.7571 (ttp-110) cc_final: 0.7209 (ttp80) REVERT: a 48 PHE cc_start: 0.6945 (t80) cc_final: 0.6595 (t80) REVERT: a 440 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7679 (tm) REVERT: a 568 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.6869 (mpt-90) REVERT: a 701 THR cc_start: 0.8708 (p) cc_final: 0.8494 (m) REVERT: a 722 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7263 (mmtm) REVERT: a 810 MET cc_start: 0.8348 (mtm) cc_final: 0.8146 (ptt) REVERT: b 78 PHE cc_start: 0.7567 (OUTLIER) cc_final: 0.7343 (t80) REVERT: c 63 ARG cc_start: 0.8676 (ptm160) cc_final: 0.8238 (ptm-80) REVERT: d 5 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7866 (tt) REVERT: d 109 TYR cc_start: 0.7988 (t80) cc_final: 0.7771 (t80) REVERT: d 293 TYR cc_start: 0.8172 (m-80) cc_final: 0.7925 (m-80) REVERT: d 295 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.6924 (t70) REVERT: e 102 GLU cc_start: 0.7558 (pt0) cc_final: 0.7296 (pt0) REVERT: e 108 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8015 (tmm) REVERT: e 110 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7388 (pt) REVERT: f 75 PHE cc_start: 0.8436 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: f 86 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7331 (mm-30) REVERT: g 64 PHE cc_start: 0.8716 (t80) cc_final: 0.8031 (t80) REVERT: g 71 ASN cc_start: 0.8701 (m110) cc_final: 0.8241 (m-40) REVERT: g 94 ARG cc_start: 0.7451 (ttp-110) cc_final: 0.7157 (ttp80) REVERT: g 100 ASN cc_start: 0.7720 (m-40) cc_final: 0.7251 (t0) outliers start: 110 outliers final: 47 residues processed: 556 average time/residue: 0.4932 time to fit residues: 341.2010 Evaluate side-chains 542 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 479 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 555 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 697 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 455 VAL Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 295 ASP Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 75 PHE Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 217 optimal weight: 5.9990 chunk 300 optimal weight: 8.9990 chunk 280 optimal weight: 0.9980 chunk 314 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 284 optimal weight: 0.2980 chunk 192 optimal weight: 0.0070 chunk 79 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 702 GLN c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN g 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.147808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.121285 restraints weight = 43162.726| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.92 r_work: 0.3399 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30962 Z= 0.134 Angle : 0.626 11.946 41942 Z= 0.316 Chirality : 0.042 0.360 4988 Planarity : 0.004 0.053 4948 Dihedral : 10.707 172.538 4650 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.78 % Allowed : 17.20 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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 (0.14), residues: 3716 helix: 2.00 (0.10), residues: 2778 sheet: -0.01 (0.59), residues: 94 loop : -2.69 (0.18), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 394 TYR 0.026 0.001 TYR A 466 PHE 0.033 0.001 PHE A 376 TRP 0.012 0.001 TRP A 298 HIS 0.003 0.001 HIS g 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (30962) covalent geometry : angle 0.62586 / 0.32 (41942) hydrogen bonds : bond 0.05087 / 3.32 ( 2167) hydrogen bonds : angle 3.90561 / 2.81 ( 6459) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 532 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.7970 (m) cc_final: 0.7527 (p) REVERT: A 123 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8851 (tm) REVERT: A 131 LYS cc_start: 0.6309 (ttpp) cc_final: 0.5907 (tttt) REVERT: A 204 MET cc_start: 0.8927 (tpp) cc_final: 0.8537 (ttp) REVERT: A 255 TYR cc_start: 0.8571 (p90) cc_final: 0.8315 (p90) REVERT: A 277 MET cc_start: 0.7817 (tpt) cc_final: 0.7387 (tpt) REVERT: A 440 LEU cc_start: 0.7887 (mt) cc_final: 0.7664 (tm) REVERT: A 516 LEU cc_start: 0.7648 (tp) cc_final: 0.7056 (mt) REVERT: A 568 ARG cc_start: 0.7942 (tpp-160) cc_final: 0.6682 (mpt-90) REVERT: A 688 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8571 (tt) REVERT: A 701 THR cc_start: 0.8579 (p) cc_final: 0.8209 (m) REVERT: A 722 LYS cc_start: 0.7934 (mmpt) cc_final: 0.7049 (mmtm) REVERT: B 9 ARG cc_start: 0.7508 (mtp180) cc_final: 0.7269 (mtm-85) REVERT: B 18 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8130 (tp) REVERT: B 78 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6614 (t80) REVERT: C 23 LYS cc_start: 0.7093 (tttt) cc_final: 0.6248 (tmmt) REVERT: C 24 SER cc_start: 0.6271 (OUTLIER) cc_final: 0.5984 (m) REVERT: C 60 LYS cc_start: 0.6958 (mttt) cc_final: 0.6492 (ttpp) REVERT: C 63 ARG cc_start: 0.8610 (ptm160) cc_final: 0.8151 (ptm-80) REVERT: D 229 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7852 (tt) REVERT: D 293 TYR cc_start: 0.8146 (m-80) cc_final: 0.7881 (m-80) REVERT: E 1 MET cc_start: 0.6852 (mpt) cc_final: 0.6584 (mtt) REVERT: E 102 GLU cc_start: 0.7271 (pt0) cc_final: 0.6847 (pt0) REVERT: E 108 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.7734 (tmm) REVERT: E 110 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7197 (pt) REVERT: E 157 SER cc_start: 0.6936 (t) cc_final: 0.6682 (m) REVERT: F 58 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7469 (mt) REVERT: G 94 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.7297 (ttp80) REVERT: a 48 PHE cc_start: 0.6999 (t80) cc_final: 0.6686 (t80) REVERT: a 78 ASP cc_start: 0.7647 (t0) cc_final: 0.7379 (t0) REVERT: a 440 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7635 (tm) REVERT: a 495 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6601 (tpp) REVERT: a 568 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.6871 (mpt-90) REVERT: a 603 SER cc_start: 0.8032 (m) cc_final: 0.7448 (p) REVERT: a 701 THR cc_start: 0.8646 (p) cc_final: 0.8422 (m) REVERT: a 722 LYS cc_start: 0.8193 (mmpt) cc_final: 0.7288 (mmtt) REVERT: b 58 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7365 (pp20) REVERT: b 78 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7342 (t80) REVERT: b 87 MET cc_start: 0.6708 (ptp) cc_final: 0.6492 (ptm) REVERT: c 63 ARG cc_start: 0.8636 (ptm160) cc_final: 0.8179 (ptm-80) REVERT: d 5 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7925 (tt) REVERT: d 293 TYR cc_start: 0.8170 (m-80) cc_final: 0.7916 (m-80) REVERT: e 31 TYR cc_start: 0.7852 (t80) cc_final: 0.7579 (t80) REVERT: e 102 GLU cc_start: 0.7543 (pt0) cc_final: 0.7235 (pt0) REVERT: e 108 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8061 (tmm) REVERT: e 110 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7353 (pt) REVERT: f 86 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7315 (mm-30) REVERT: g 71 ASN cc_start: 0.8685 (m110) cc_final: 0.8229 (m-40) REVERT: g 81 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8195 (pt) REVERT: g 94 ARG cc_start: 0.7379 (ttp-110) cc_final: 0.7080 (ttp80) REVERT: g 100 ASN cc_start: 0.7681 (m-40) cc_final: 0.7216 (t0) outliers start: 87 outliers final: 44 residues processed: 579 average time/residue: 0.5073 time to fit residues: 364.0574 Evaluate side-chains 557 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 496 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 192 LYS Chi-restraints excluded: chain a residue 218 TYR Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 455 VAL Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 81 ILE Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 218 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 314 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 342 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 294 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 300 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN a 702 GLN c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.144641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.117771 restraints weight = 43083.016| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.91 r_work: 0.3349 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30962 Z= 0.177 Angle : 0.688 11.946 41942 Z= 0.348 Chirality : 0.045 0.374 4988 Planarity : 0.005 0.051 4948 Dihedral : 10.806 170.244 4650 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.97 % Allowed : 17.65 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.14), residues: 3716 helix: 1.91 (0.10), residues: 2770 sheet: 0.00 (0.58), residues: 94 loop : -2.66 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 394 TYR 0.022 0.002 TYR b 122 PHE 0.030 0.002 PHE A 376 TRP 0.011 0.001 TRP A 298 HIS 0.008 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (30962) covalent geometry : angle 0.68834 / 0.35 (41942) hydrogen bonds : bond 0.05765 / 3.76 ( 2167) hydrogen bonds : angle 4.03110 / 2.91 ( 6459) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 504 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8089 (m) cc_final: 0.7512 (p) REVERT: A 123 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8812 (tm) REVERT: A 131 LYS cc_start: 0.6339 (ttpp) cc_final: 0.5861 (tttt) REVERT: A 194 MET cc_start: 0.7291 (ttp) cc_final: 0.7074 (ttp) REVERT: A 277 MET cc_start: 0.7802 (tpt) cc_final: 0.7323 (tpt) REVERT: A 440 LEU cc_start: 0.7952 (mt) cc_final: 0.7736 (tp) REVERT: A 516 LEU cc_start: 0.7740 (tp) cc_final: 0.7155 (mt) REVERT: A 568 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.6715 (mpt-90) REVERT: A 688 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8611 (tt) REVERT: A 701 THR cc_start: 0.8585 (p) cc_final: 0.8207 (m) REVERT: A 722 LYS cc_start: 0.7913 (mmpt) cc_final: 0.7042 (mmtm) REVERT: B 18 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8210 (tp) REVERT: B 78 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6656 (t80) REVERT: C 11 CYS cc_start: 0.8436 (t) cc_final: 0.7756 (m) REVERT: C 23 LYS cc_start: 0.7151 (tttt) cc_final: 0.6321 (tmmt) REVERT: C 60 LYS cc_start: 0.6996 (mttt) cc_final: 0.6515 (ttpp) REVERT: C 63 ARG cc_start: 0.8624 (ptm160) cc_final: 0.8155 (ptm-80) REVERT: D 229 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7955 (tt) REVERT: D 293 TYR cc_start: 0.8180 (m-80) cc_final: 0.7860 (m-80) REVERT: D 461 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8414 (mp) REVERT: D 464 GLU cc_start: 0.8731 (tp30) cc_final: 0.8455 (tp30) REVERT: E 77 LYS cc_start: 0.7991 (ttpt) cc_final: 0.7755 (tmmt) REVERT: E 108 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7751 (tmm) REVERT: E 110 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7231 (pt) REVERT: E 157 SER cc_start: 0.6950 (t) cc_final: 0.6594 (m) REVERT: F 58 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7642 (mt) REVERT: G 94 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7309 (ttp80) REVERT: a 48 PHE cc_start: 0.6975 (t80) cc_final: 0.6643 (t80) REVERT: a 143 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8700 (tp) REVERT: a 440 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7659 (tm) REVERT: a 495 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.7001 (tpp) REVERT: a 568 ARG cc_start: 0.8081 (tpp-160) cc_final: 0.6860 (mpt-90) REVERT: a 701 THR cc_start: 0.8741 (p) cc_final: 0.8478 (m) REVERT: a 722 LYS cc_start: 0.8185 (mmpt) cc_final: 0.7290 (mmtt) REVERT: b 58 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7404 (pp20) REVERT: b 62 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8122 (ttpp) REVERT: b 78 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7351 (t80) REVERT: c 11 CYS cc_start: 0.8572 (t) cc_final: 0.7803 (m) REVERT: c 63 ARG cc_start: 0.8646 (ptm160) cc_final: 0.8181 (ptm-80) REVERT: d 5 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7994 (tt) REVERT: d 293 TYR cc_start: 0.8207 (m-80) cc_final: 0.7959 (m-80) REVERT: e 102 GLU cc_start: 0.7564 (pt0) cc_final: 0.7271 (pt0) REVERT: e 108 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8050 (tmm) REVERT: e 110 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7374 (pt) REVERT: f 75 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: f 86 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7341 (mm-30) REVERT: g 71 ASN cc_start: 0.8720 (m110) cc_final: 0.8278 (m-40) REVERT: g 94 ARG cc_start: 0.7431 (ttp-110) cc_final: 0.7145 (ttp80) REVERT: g 100 ASN cc_start: 0.7726 (m-40) cc_final: 0.7241 (t0) outliers start: 93 outliers final: 48 residues processed: 550 average time/residue: 0.5200 time to fit residues: 353.3515 Evaluate side-chains 546 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 479 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain G residue 81 ILE Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 143 LEU Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 555 MET Chi-restraints excluded: chain a residue 618 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 697 ASP Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 62 LYS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 5 LEU Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 75 ASP Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain f residue 37 MET Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain f residue 75 PHE Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 262 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 340 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 143 optimal weight: 0.7980 chunk 158 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 702 GLN c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN g 10 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.147018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.120290 restraints weight = 43184.294| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.92 r_work: 0.3385 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 30962 Z= 0.145 Angle : 0.666 12.500 41942 Z= 0.335 Chirality : 0.043 0.381 4988 Planarity : 0.004 0.051 4948 Dihedral : 10.581 166.291 4650 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.33 % Allowed : 18.67 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.43 (0.14), residues: 3716 helix: 2.00 (0.10), residues: 2782 sheet: -0.01 (0.58), residues: 94 loop : -2.72 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 394 TYR 0.024 0.001 TYR A 466 PHE 0.032 0.001 PHE A 376 TRP 0.013 0.001 TRP a 166 HIS 0.007 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (30962) covalent geometry : angle 0.66553 / 0.34 (41942) hydrogen bonds : bond 0.05302 / 3.46 ( 2167) hydrogen bonds : angle 3.96709 / 2.87 ( 6459) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 500 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.8020 (m) cc_final: 0.7414 (p) REVERT: A 123 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8805 (tm) REVERT: A 131 LYS cc_start: 0.6272 (ttpp) cc_final: 0.5881 (tttt) REVERT: A 277 MET cc_start: 0.7782 (tpt) cc_final: 0.7381 (tpt) REVERT: A 439 MET cc_start: 0.7066 (pp-130) cc_final: 0.6808 (ppp) REVERT: A 440 LEU cc_start: 0.7885 (mt) cc_final: 0.7521 (tp) REVERT: A 516 LEU cc_start: 0.7725 (tp) cc_final: 0.7156 (mt) REVERT: A 568 ARG cc_start: 0.7900 (tpp-160) cc_final: 0.6647 (mpt-90) REVERT: A 688 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8576 (tt) REVERT: A 701 THR cc_start: 0.8584 (p) cc_final: 0.8212 (m) REVERT: A 722 LYS cc_start: 0.7895 (mmpt) cc_final: 0.7010 (mmtm) REVERT: B 18 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8136 (tp) REVERT: B 78 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6616 (t80) REVERT: C 11 CYS cc_start: 0.8394 (t) cc_final: 0.7716 (m) REVERT: C 23 LYS cc_start: 0.7131 (tttt) cc_final: 0.6324 (tmmt) REVERT: C 24 SER cc_start: 0.6301 (OUTLIER) cc_final: 0.6074 (m) REVERT: C 60 LYS cc_start: 0.6931 (mttt) cc_final: 0.6451 (ttpp) REVERT: C 63 ARG cc_start: 0.8625 (ptm160) cc_final: 0.8154 (ptm-80) REVERT: D 197 ASN cc_start: 0.8334 (m-40) cc_final: 0.7980 (t0) REVERT: D 229 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7911 (tt) REVERT: D 293 TYR cc_start: 0.8168 (m-80) cc_final: 0.7929 (m-80) REVERT: D 464 GLU cc_start: 0.8680 (tp30) cc_final: 0.8295 (tp30) REVERT: E 77 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7780 (tmmt) REVERT: E 108 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.7770 (tmm) REVERT: E 110 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7194 (pt) REVERT: E 157 SER cc_start: 0.6934 (t) cc_final: 0.6608 (m) REVERT: F 14 MET cc_start: 0.7738 (tpp) cc_final: 0.7502 (tpp) REVERT: F 58 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7499 (mt) REVERT: G 94 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7303 (ttp80) REVERT: a 48 PHE cc_start: 0.6934 (t80) cc_final: 0.6611 (t80) REVERT: a 78 ASP cc_start: 0.7635 (t0) cc_final: 0.7359 (t0) REVERT: a 143 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8635 (tp) REVERT: a 440 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7652 (tm) REVERT: a 495 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.7007 (tpp) REVERT: a 568 ARG cc_start: 0.8047 (tpp-160) cc_final: 0.6857 (mpt-90) REVERT: a 603 SER cc_start: 0.8043 (m) cc_final: 0.7456 (p) REVERT: a 701 THR cc_start: 0.8734 (p) cc_final: 0.8432 (m) REVERT: a 722 LYS cc_start: 0.8179 (mmpt) cc_final: 0.7283 (mmtt) REVERT: b 58 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7383 (pp20) REVERT: c 11 CYS cc_start: 0.8574 (t) cc_final: 0.7803 (m) REVERT: c 63 ARG cc_start: 0.8614 (ptm160) cc_final: 0.8153 (ptm-80) REVERT: d 109 TYR cc_start: 0.7842 (t80) cc_final: 0.7622 (t80) REVERT: d 293 TYR cc_start: 0.8194 (m-80) cc_final: 0.7936 (m-80) REVERT: e 102 GLU cc_start: 0.7556 (pt0) cc_final: 0.7217 (pt0) REVERT: e 108 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8063 (tmm) REVERT: e 110 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7366 (pt) REVERT: f 86 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7297 (mm-30) REVERT: g 71 ASN cc_start: 0.8692 (m110) cc_final: 0.8254 (m-40) REVERT: g 94 ARG cc_start: 0.7381 (ttp-110) cc_final: 0.7087 (ttp80) REVERT: g 100 ASN cc_start: 0.7671 (m-40) cc_final: 0.7209 (t0) outliers start: 73 outliers final: 40 residues processed: 535 average time/residue: 0.5170 time to fit residues: 342.2115 Evaluate side-chains 541 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 486 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 143 LEU Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 162 optimal weight: 0.4980 chunk 204 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 274 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 176 optimal weight: 0.7980 chunk 242 optimal weight: 5.9990 chunk 302 optimal weight: 4.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN c 96 GLN d 57 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.147250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.120561 restraints weight = 42930.119| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.92 r_work: 0.3389 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30962 Z= 0.149 Angle : 0.673 14.179 41942 Z= 0.338 Chirality : 0.044 0.387 4988 Planarity : 0.004 0.051 4948 Dihedral : 10.493 164.320 4650 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.91 % Allowed : 19.24 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.43 (0.14), residues: 3716 helix: 1.99 (0.10), residues: 2782 sheet: 0.02 (0.58), residues: 94 loop : -2.70 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG a 394 TYR 0.023 0.001 TYR A 466 PHE 0.032 0.001 PHE A 376 TRP 0.013 0.001 TRP a 166 HIS 0.009 0.001 HIS A 389 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (30962) covalent geometry : angle 0.67278 / 0.34 (41942) hydrogen bonds : bond 0.05296 / 3.46 ( 2167) hydrogen bonds : angle 3.96621 / 2.86 ( 6459) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 502 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.7996 (m) cc_final: 0.7388 (p) REVERT: A 123 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8828 (tm) REVERT: A 131 LYS cc_start: 0.6299 (ttpp) cc_final: 0.5896 (tttt) REVERT: A 277 MET cc_start: 0.7775 (tpt) cc_final: 0.7384 (tpt) REVERT: A 439 MET cc_start: 0.7030 (pp-130) cc_final: 0.6716 (ppp) REVERT: A 440 LEU cc_start: 0.7865 (mt) cc_final: 0.7546 (tp) REVERT: A 516 LEU cc_start: 0.7706 (tp) cc_final: 0.7142 (mt) REVERT: A 568 ARG cc_start: 0.7890 (tpp-160) cc_final: 0.6640 (mpt-90) REVERT: A 688 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8580 (tt) REVERT: A 722 LYS cc_start: 0.7900 (mmpt) cc_final: 0.7006 (mmtm) REVERT: B 18 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8127 (tp) REVERT: B 78 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.6624 (t80) REVERT: C 11 CYS cc_start: 0.8380 (t) cc_final: 0.7706 (m) REVERT: C 23 LYS cc_start: 0.7134 (tttt) cc_final: 0.6336 (tmmt) REVERT: C 24 SER cc_start: 0.6214 (OUTLIER) cc_final: 0.5998 (m) REVERT: C 60 LYS cc_start: 0.6890 (mttt) cc_final: 0.6406 (ttpp) REVERT: C 63 ARG cc_start: 0.8616 (ptm160) cc_final: 0.8153 (ptm-80) REVERT: D 197 ASN cc_start: 0.8337 (m-40) cc_final: 0.7969 (t0) REVERT: D 229 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7913 (tt) REVERT: D 293 TYR cc_start: 0.8166 (m-80) cc_final: 0.7928 (m-80) REVERT: D 464 GLU cc_start: 0.8669 (tp30) cc_final: 0.8278 (tp30) REVERT: E 77 LYS cc_start: 0.8007 (ttpt) cc_final: 0.7760 (tmmt) REVERT: E 102 GLU cc_start: 0.7239 (pt0) cc_final: 0.6782 (pt0) REVERT: E 108 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7781 (tmm) REVERT: E 110 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7183 (pt) REVERT: E 154 MET cc_start: 0.7196 (mtm) cc_final: 0.6769 (mmm) REVERT: E 157 SER cc_start: 0.6934 (t) cc_final: 0.6619 (m) REVERT: F 14 MET cc_start: 0.7751 (tpp) cc_final: 0.7537 (tpp) REVERT: F 58 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7455 (mt) REVERT: G 94 ARG cc_start: 0.7560 (ttp-110) cc_final: 0.7305 (ttp80) REVERT: a 48 PHE cc_start: 0.6949 (t80) cc_final: 0.6622 (t80) REVERT: a 78 ASP cc_start: 0.7648 (t0) cc_final: 0.7409 (t0) REVERT: a 143 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8636 (tp) REVERT: a 440 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7641 (tm) REVERT: a 495 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.7023 (tpp) REVERT: a 568 ARG cc_start: 0.8048 (tpp-160) cc_final: 0.6862 (mpt-90) REVERT: a 603 SER cc_start: 0.8083 (m) cc_final: 0.7501 (p) REVERT: a 644 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7635 (ttm170) REVERT: a 701 THR cc_start: 0.8709 (p) cc_final: 0.8392 (m) REVERT: a 722 LYS cc_start: 0.8178 (mmpt) cc_final: 0.7274 (mmtt) REVERT: b 58 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7377 (pp20) REVERT: c 11 CYS cc_start: 0.8565 (t) cc_final: 0.7792 (m) REVERT: c 63 ARG cc_start: 0.8621 (ptm160) cc_final: 0.8152 (ptm-80) REVERT: d 109 TYR cc_start: 0.7899 (t80) cc_final: 0.7674 (t80) REVERT: d 293 TYR cc_start: 0.8184 (m-80) cc_final: 0.7933 (m-80) REVERT: e 102 GLU cc_start: 0.7552 (pt0) cc_final: 0.7217 (pt0) REVERT: e 108 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8062 (tmm) REVERT: e 110 ILE cc_start: 0.7773 (OUTLIER) cc_final: 0.7359 (pt) REVERT: f 86 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7298 (mm-30) REVERT: g 71 ASN cc_start: 0.8685 (m110) cc_final: 0.8242 (m-40) REVERT: g 94 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.7089 (ttp80) REVERT: g 100 ASN cc_start: 0.7697 (m-40) cc_final: 0.7201 (t0) outliers start: 60 outliers final: 39 residues processed: 532 average time/residue: 0.5155 time to fit residues: 339.0808 Evaluate side-chains 541 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 486 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 792 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 78 PHE Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 476 VAL Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 110 ILE Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 59 ASP Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 143 LEU Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 644 ARG Chi-restraints excluded: chain a residue 667 VAL Chi-restraints excluded: chain a residue 715 LEU Chi-restraints excluded: chain b residue 31 HIS Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 85 SER Chi-restraints excluded: chain c residue 32 THR Chi-restraints excluded: chain d residue 137 GLU Chi-restraints excluded: chain d residue 476 VAL Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 108 MET Chi-restraints excluded: chain e residue 110 ILE Chi-restraints excluded: chain e residue 111 THR Chi-restraints excluded: chain e residue 116 THR Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 59 ASP Chi-restraints excluded: chain g residue 98 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 196 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 315 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 349 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 287 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN g 10 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.147302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120611 restraints weight = 43323.145| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.93 r_work: 0.3392 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30962 Z= 0.147 Angle : 0.674 14.062 41942 Z= 0.339 Chirality : 0.043 0.387 4988 Planarity : 0.004 0.051 4948 Dihedral : 10.422 162.786 4650 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.30 % Allowed : 19.18 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.42 (0.14), residues: 3716 helix: 1.98 (0.10), residues: 2790 sheet: 0.02 (0.58), residues: 94 loop : -2.74 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 394 TYR 0.024 0.001 TYR A 466 PHE 0.032 0.001 PHE A 376 TRP 0.013 0.001 TRP a 166 HIS 0.005 0.001 HIS D 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (30962) covalent geometry : angle 0.67409 / 0.34 (41942) hydrogen bonds : bond 0.05251 / 3.43 ( 2167) hydrogen bonds : angle 3.96628 / 2.87 ( 6459) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11073.78 seconds wall clock time: 189 minutes 15.41 seconds (11355.41 seconds total)