Starting phenix.real_space_refine on Wed Jun 25 12:54:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6z16_11027/06_2025/6z16_11027.cif Found real_map, /net/cci-nas-00/data/ceres_data/6z16_11027/06_2025/6z16_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_11027/06_2025/6z16_11027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6z16_11027/06_2025/6z16_11027.map" model { file = "/net/cci-nas-00/data/ceres_data/6z16_11027/06_2025/6z16_11027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6z16_11027/06_2025/6z16_11027.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.58, per 1000 atoms: 0.55 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: 7.94 Conformation dependent library (CDL) restraints added in 3.6 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: 3.25 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: 10.30 Time building geometry restraints manager: 9.05 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: 17819 34.92 - 69.84: 209 69.84 - 104.77: 37 104.77 - 139.69: 10 139.69 - 174.61: 5 Dihedral angle restraints: 18080 sinusoidal: 7240 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 18077 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: 0.310 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: 0.020 Extract box with map and model: 1.340 Check model and map are aligned: 0.240 Set scattering table: 0.290 Process input model: 63.040 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 13.193 174.609 11120 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.004 TRP a 166 HIS 0.013 0.002 HIS D 272 PHE 0.047 0.004 PHE c 87 TYR 0.040 0.003 TYR A 619 ARG 0.010 0.001 ARG a 473 Details of bonding type rmsd hydrogen bonds : bond 0.14082 ( 2167) hydrogen bonds : angle 5.79949 ( 6459) covalent geometry : bond 0.00819 (30962) covalent geometry : angle 1.13469 (41942) *********************** 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 : 3.157 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: 0.5733 (p0) REVERT: A 372 ASN cc_start: 0.8244 (t0) cc_final: 0.7994 (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: 0.6839 (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: 0.6922 (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: 0.7281 (mttm) REVERT: e 83 SER cc_start: 0.7017 (m) cc_final: 0.6678 (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: 0.7230 (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: 1.1581 time to fit residues: 1091.4643 Evaluate side-chains 492 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 3.371 ------------------------------------------------------------------------------- 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 307 optimal weight: 6.9990 chunk 275 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 330 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 HIS A 320 GLN A 547 HIS ** A 635 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN C 102 HIS D 155 GLN 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 759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 155 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119460 restraints weight = 42782.183| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.87 r_work: 0.3373 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30962 Z= 0.174 Angle : 0.688 10.977 41942 Z= 0.357 Chirality : 0.044 0.228 4988 Planarity : 0.006 0.055 4948 Dihedral : 13.695 170.950 4808 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.10 % Allowed : 10.94 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3716 helix: 0.77 (0.09), residues: 2768 sheet: -0.46 (0.56), residues: 90 loop : -3.07 (0.17), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 166 HIS 0.006 0.001 HIS D 272 PHE 0.033 0.002 PHE A 376 TYR 0.030 0.002 TYR a 466 ARG 0.007 0.001 ARG a 394 Details of bonding type rmsd hydrogen bonds : bond 0.06494 ( 2167) hydrogen bonds : angle 4.34606 ( 6459) covalent geometry : bond 0.00378 (30962) covalent geometry : angle 0.68760 (41942) *********************** 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 652 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 555 time to evaluate : 3.212 Fit side-chains REVERT: A 94 SER cc_start: 0.8289 (m) cc_final: 0.7741 (p) REVERT: A 131 LYS cc_start: 0.6403 (ttpp) cc_final: 0.5942 (tttt) REVERT: A 372 ASN cc_start: 0.8398 (t0) cc_final: 0.7967 (m110) REVERT: A 435 PHE cc_start: 0.7350 (t80) cc_final: 0.7146 (t80) REVERT: A 440 LEU cc_start: 0.8016 (mt) cc_final: 0.7257 (tm) REVERT: A 568 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.6820 (mpt-90) REVERT: A 701 THR cc_start: 0.8600 (p) cc_final: 0.8127 (m) REVERT: A 722 LYS cc_start: 0.8004 (mmpt) cc_final: 0.7067 (mmtm) REVERT: B 78 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6871 (t80) REVERT: C 60 LYS cc_start: 0.7218 (mttt) cc_final: 0.6760 (ttpp) REVERT: C 63 ARG cc_start: 0.8840 (ptm160) cc_final: 0.8391 (ptm-80) REVERT: D 293 TYR cc_start: 0.8254 (m-80) cc_final: 0.7957 (m-80) REVERT: D 318 MET cc_start: 0.6670 (mmp) cc_final: 0.5708 (pmt) REVERT: E 110 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7324 (pt) REVERT: G 100 ASN cc_start: 0.7232 (m-40) cc_final: 0.6930 (t0) REVERT: a 48 PHE cc_start: 0.6964 (t80) cc_final: 0.6668 (t80) REVERT: a 372 ASN cc_start: 0.8448 (t0) cc_final: 0.8175 (m110) REVERT: a 440 LEU cc_start: 0.8219 (mm) cc_final: 0.7522 (tm) REVERT: a 568 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.6971 (mpt-90) REVERT: b 100 TYR cc_start: 0.7377 (m-80) cc_final: 0.7112 (m-80) REVERT: c 60 LYS cc_start: 0.7278 (mttt) cc_final: 0.6839 (ttpp) REVERT: c 63 ARG cc_start: 0.8781 (ptm160) cc_final: 0.8386 (ptm-80) REVERT: d 137 GLU cc_start: 0.7866 (mp0) cc_final: 0.7551 (mp0) REVERT: d 485 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: e 99 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7918 (ptmt) REVERT: e 102 GLU cc_start: 0.7691 (pt0) cc_final: 0.7112 (pt0) REVERT: e 108 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8007 (tmm) REVERT: f 86 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7362 (mm-30) REVERT: g 100 ASN cc_start: 0.7774 (m-40) cc_final: 0.7361 (t0) outliers start: 97 outliers final: 38 residues processed: 604 average time/residue: 1.0958 time to fit residues: 814.5719 Evaluate side-chains 520 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 478 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE 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 59 LEU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 187 LEU 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 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 154 MET Chi-restraints excluded: chain G residue 72 SER 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 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 c residue 62 SER Chi-restraints excluded: chain d residue 58 THR Chi-restraints excluded: chain d residue 59 LEU Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 485 GLU Chi-restraints excluded: chain d residue 489 LYS Chi-restraints excluded: chain e residue 38 LEU Chi-restraints excluded: chain e residue 87 GLN 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 g residue 13 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 18 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 181 optimal weight: 0.0060 chunk 248 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 206 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 overall best weight: 3.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 3 ASN D 29 GLN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 191 GLN a 610 ASN a 733 HIS ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119351 restraints weight = 42944.228| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.86 r_work: 0.3371 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2022 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= 0.160 Angle : 0.658 10.904 41942 Z= 0.338 Chirality : 0.043 0.354 4988 Planarity : 0.005 0.054 4948 Dihedral : 13.146 157.502 4806 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.83 % Allowed : 12.80 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3716 helix: 1.45 (0.10), residues: 2756 sheet: -0.18 (0.58), residues: 90 loop : -2.88 (0.17), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 166 HIS 0.006 0.001 HIS D 272 PHE 0.034 0.002 PHE A 376 TYR 0.028 0.002 TYR A 466 ARG 0.005 0.001 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.05936 ( 2167) hydrogen bonds : angle 4.14257 ( 6459) covalent geometry : bond 0.00358 (30962) covalent geometry : angle 0.65808 (41942) *********************** 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 661 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 541 time to evaluate : 3.324 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8146 (m) cc_final: 0.7703 (p) REVERT: A 131 LYS cc_start: 0.6416 (ttpp) cc_final: 0.5949 (tttt) REVERT: A 354 MET cc_start: 0.6607 (pmm) cc_final: 0.6238 (tpp) REVERT: A 372 ASN cc_start: 0.8384 (t0) cc_final: 0.8028 (m110) REVERT: A 440 LEU cc_start: 0.7960 (mt) cc_final: 0.7588 (tm) REVERT: A 568 ARG cc_start: 0.8025 (tpp-160) cc_final: 0.6796 (mpt-90) REVERT: A 688 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8637 (tt) REVERT: A 701 THR cc_start: 0.8614 (p) cc_final: 0.8181 (m) REVERT: A 722 LYS cc_start: 0.7983 (mmpt) cc_final: 0.7041 (mmtm) REVERT: B 78 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6892 (t80) REVERT: C 60 LYS cc_start: 0.7087 (mttt) cc_final: 0.6664 (ttpp) REVERT: C 63 ARG cc_start: 0.8774 (ptm160) cc_final: 0.8319 (ptm-80) REVERT: D 5 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7945 (tt) REVERT: D 229 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8041 (tt) REVERT: D 293 TYR cc_start: 0.8246 (m-80) cc_final: 0.7979 (m-80) REVERT: D 318 MET cc_start: 0.6872 (mmp) cc_final: 0.5774 (pmm) REVERT: E 110 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7357 (pt) REVERT: E 157 SER cc_start: 0.6972 (t) cc_final: 0.6647 (m) REVERT: F 58 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7727 (mt) REVERT: G 100 ASN cc_start: 0.7237 (m-40) cc_final: 0.6935 (t0) REVERT: a 48 PHE cc_start: 0.6940 (t80) cc_final: 0.6633 (t80) REVERT: a 78 ASP cc_start: 0.7686 (t0) cc_final: 0.7455 (t0) REVERT: a 440 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7519 (tm) REVERT: a 567 TYR cc_start: 0.8221 (t80) cc_final: 0.7983 (t80) REVERT: a 568 ARG cc_start: 0.8143 (tpp-160) cc_final: 0.7026 (mpt-90) REVERT: a 609 MET cc_start: 0.8237 (mmt) cc_final: 0.8006 (mmt) REVERT: a 701 THR cc_start: 0.8762 (p) cc_final: 0.8412 (m) REVERT: a 722 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7128 (mmtm) REVERT: b 62 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8111 (ttpp) REVERT: b 78 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7213 (t80) REVERT: c 60 LYS cc_start: 0.7202 (mttt) cc_final: 0.6796 (ttpp) REVERT: c 63 ARG cc_start: 0.8736 (ptm160) cc_final: 0.8301 (ptm-80) REVERT: d 5 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7934 (tt) REVERT: d 76 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.8068 (m) REVERT: d 405 ILE cc_start: 0.8546 (mm) cc_final: 0.8261 (mt) REVERT: e 102 GLU cc_start: 0.7744 (pt0) cc_final: 0.7160 (pt0) REVERT: e 108 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7990 (tmm) REVERT: e 110 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7313 (pt) REVERT: f 86 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7365 (mm-30) REVERT: g 71 ASN cc_start: 0.8597 (m110) cc_final: 0.8161 (m-40) REVERT: g 100 ASN cc_start: 0.7764 (m-40) cc_final: 0.7359 (t0) outliers start: 120 outliers final: 39 residues processed: 601 average time/residue: 1.0669 time to fit residues: 793.2066 Evaluate side-chains 542 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 490 time to evaluate : 3.165 ------------------------------------------------------------------------------- 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 417 SER Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 745 MET 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 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 229 LEU Chi-restraints excluded: chain D residue 296 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 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 58 LEU 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 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 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 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 85 SER Chi-restraints excluded: chain c residue 24 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 76 SER 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 g residue 13 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 77 optimal weight: 1.9990 chunk 278 optimal weight: 0.3980 chunk 249 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 372 ASN b 96 HIS d 3 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.146926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.120496 restraints weight = 43066.912| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.86 r_work: 0.3388 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30962 Z= 0.143 Angle : 0.634 13.675 41942 Z= 0.322 Chirality : 0.042 0.362 4988 Planarity : 0.005 0.054 4948 Dihedral : 12.635 161.540 4806 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.77 % Allowed : 13.37 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3716 helix: 1.73 (0.10), residues: 2772 sheet: -0.00 (0.59), residues: 90 loop : -2.87 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 166 HIS 0.006 0.001 HIS D 272 PHE 0.033 0.002 PHE A 376 TYR 0.025 0.002 TYR a 466 ARG 0.010 0.001 ARG a 649 Details of bonding type rmsd hydrogen bonds : bond 0.05445 ( 2167) hydrogen bonds : angle 4.01833 ( 6459) covalent geometry : bond 0.00307 (30962) covalent geometry : angle 0.63385 (41942) *********************** 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 670 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 552 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.8147 (m) cc_final: 0.7546 (p) REVERT: A 123 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8834 (tm) REVERT: A 131 LYS cc_start: 0.6419 (ttpp) cc_final: 0.5921 (tttt) REVERT: A 354 MET cc_start: 0.6750 (pmm) cc_final: 0.6323 (tpp) REVERT: A 372 ASN cc_start: 0.8381 (t0) cc_final: 0.8158 (m110) REVERT: A 440 LEU cc_start: 0.7930 (mt) cc_final: 0.7603 (tm) REVERT: A 568 ARG cc_start: 0.8010 (tpp-160) cc_final: 0.6782 (mpt-90) REVERT: A 688 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8551 (tt) REVERT: A 701 THR cc_start: 0.8602 (p) cc_final: 0.8217 (m) REVERT: A 722 LYS cc_start: 0.7996 (mmpt) cc_final: 0.7077 (mmtm) REVERT: B 134 GLU cc_start: 0.7601 (pt0) cc_final: 0.7395 (tt0) REVERT: C 60 LYS cc_start: 0.6985 (mttt) cc_final: 0.6598 (ttpp) REVERT: C 63 ARG cc_start: 0.8741 (ptm160) cc_final: 0.8283 (ptm-80) REVERT: D 5 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7938 (tt) REVERT: D 229 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7940 (tt) REVERT: D 293 TYR cc_start: 0.8208 (m-80) cc_final: 0.7906 (m-80) REVERT: D 318 MET cc_start: 0.6923 (mmp) cc_final: 0.5771 (pmm) REVERT: D 464 GLU cc_start: 0.8654 (tp30) cc_final: 0.8400 (tp30) REVERT: E 108 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7703 (tmm) REVERT: E 110 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7343 (pt) REVERT: E 157 SER cc_start: 0.7015 (t) cc_final: 0.6694 (m) REVERT: F 58 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7640 (mt) REVERT: G 94 ARG cc_start: 0.7532 (ttp-110) cc_final: 0.7229 (ttp80) REVERT: G 100 ASN cc_start: 0.7226 (m-40) cc_final: 0.6932 (t0) REVERT: a 48 PHE cc_start: 0.6947 (t80) cc_final: 0.6642 (t80) REVERT: a 78 ASP cc_start: 0.7624 (t0) cc_final: 0.7385 (t0) REVERT: a 372 ASN cc_start: 0.8422 (m-40) cc_final: 0.8218 (m-40) REVERT: a 440 LEU cc_start: 0.8235 (mm) cc_final: 0.7609 (tm) REVERT: a 567 TYR cc_start: 0.8271 (t80) cc_final: 0.8041 (t80) REVERT: a 568 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7007 (mpt-90) REVERT: a 701 THR cc_start: 0.8731 (p) cc_final: 0.8430 (m) REVERT: a 722 LYS cc_start: 0.8195 (mmpt) cc_final: 0.7200 (mmtm) REVERT: b 62 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8085 (ttpp) REVERT: b 78 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7236 (t80) REVERT: c 60 LYS cc_start: 0.7174 (mttt) cc_final: 0.6798 (ttpp) REVERT: c 63 ARG cc_start: 0.8694 (ptm160) cc_final: 0.8279 (ptm-80) REVERT: d 5 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7855 (tt) REVERT: d 76 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (m) REVERT: d 405 ILE cc_start: 0.8502 (mm) cc_final: 0.8273 (mt) REVERT: e 102 GLU cc_start: 0.7743 (pt0) cc_final: 0.7238 (pt0) REVERT: e 108 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8026 (tmm) REVERT: e 110 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7340 (pt) REVERT: f 86 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7368 (mm-30) REVERT: g 64 PHE cc_start: 0.8711 (t80) cc_final: 0.7921 (t80) REVERT: g 71 ASN cc_start: 0.8599 (m110) cc_final: 0.8170 (m-40) REVERT: g 100 ASN cc_start: 0.7761 (m-40) cc_final: 0.7325 (t0) outliers start: 118 outliers final: 44 residues processed: 615 average time/residue: 1.1319 time to fit residues: 862.2599 Evaluate side-chains 541 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 484 time to evaluate : 3.398 ------------------------------------------------------------------------------- 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 455 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 296 MET 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 G residue 15 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 72 SER Chi-restraints excluded: chain a residue 33 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 258 LEU 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 24 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 58 THR Chi-restraints excluded: chain d residue 76 SER Chi-restraints excluded: chain d residue 318 MET 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 g residue 98 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 141 optimal weight: 7.9990 chunk 276 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 219 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 733 HIS D 303 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN c 96 GLN d 303 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 10 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114471 restraints weight = 43337.644| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.84 r_work: 0.3313 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2470 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= 0.218 Angle : 0.726 11.898 41942 Z= 0.368 Chirality : 0.047 0.357 4988 Planarity : 0.005 0.061 4948 Dihedral : 12.884 164.407 4806 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.02 % Allowed : 14.52 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3716 helix: 1.63 (0.10), residues: 2754 sheet: -0.27 (0.57), residues: 94 loop : -2.80 (0.18), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 371 HIS 0.012 0.002 HIS D 272 PHE 0.030 0.002 PHE A 376 TYR 0.021 0.002 TYR a 755 ARG 0.007 0.001 ARG A 644 Details of bonding type rmsd hydrogen bonds : bond 0.06523 ( 2167) hydrogen bonds : angle 4.20148 ( 6459) covalent geometry : bond 0.00520 (30962) covalent geometry : angle 0.72558 (41942) *********************** 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 631 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 505 time to evaluate : 3.410 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8165 (m) cc_final: 0.7539 (p) REVERT: A 123 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8821 (tm) REVERT: A 131 LYS cc_start: 0.6354 (ttpp) cc_final: 0.5903 (tttt) REVERT: A 372 ASN cc_start: 0.8413 (t0) cc_final: 0.8204 (m110) REVERT: A 440 LEU cc_start: 0.7923 (mt) cc_final: 0.7629 (tm) REVERT: A 568 ARG cc_start: 0.8073 (tpp-160) cc_final: 0.6843 (mpt-90) REVERT: A 688 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8662 (tt) REVERT: A 701 THR cc_start: 0.8594 (p) cc_final: 0.8317 (m) REVERT: A 722 LYS cc_start: 0.7962 (mmpt) cc_final: 0.7073 (mmtm) REVERT: B 18 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8266 (tp) REVERT: C 60 LYS cc_start: 0.7102 (mttt) cc_final: 0.6726 (ttpp) REVERT: C 63 ARG cc_start: 0.8733 (ptm160) cc_final: 0.8294 (ptm-80) REVERT: D 5 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7997 (tt) REVERT: D 229 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8031 (tt) REVERT: D 293 TYR cc_start: 0.8308 (m-80) cc_final: 0.8008 (m-80) REVERT: E 64 PHE cc_start: 0.7012 (m-10) cc_final: 0.6696 (m-10) REVERT: E 108 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.7770 (tmm) REVERT: E 110 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7370 (pt) REVERT: E 119 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7770 (pp) REVERT: E 157 SER cc_start: 0.7047 (t) cc_final: 0.6689 (m) REVERT: a 48 PHE cc_start: 0.6916 (t80) cc_final: 0.6610 (t80) REVERT: a 440 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7542 (tm) REVERT: a 567 TYR cc_start: 0.8472 (t80) cc_final: 0.8241 (t80) REVERT: a 568 ARG cc_start: 0.8139 (tpp-160) cc_final: 0.6981 (mpt-90) REVERT: a 594 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: a 701 THR cc_start: 0.8768 (p) cc_final: 0.8512 (m) REVERT: a 722 LYS cc_start: 0.8244 (mmpt) cc_final: 0.7294 (mmtm) REVERT: b 62 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8117 (ttpp) REVERT: b 78 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7376 (t80) REVERT: c 60 LYS cc_start: 0.7337 (mttt) cc_final: 0.6952 (ttpp) REVERT: c 63 ARG cc_start: 0.8746 (ptm160) cc_final: 0.8299 (ptm-80) REVERT: d 5 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7941 (tt) REVERT: d 293 TYR cc_start: 0.8219 (m-80) cc_final: 0.7977 (m-80) REVERT: d 405 ILE cc_start: 0.8684 (mm) cc_final: 0.8392 (mt) REVERT: d 446 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8217 (tt) REVERT: e 108 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8159 (tmm) REVERT: e 110 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7508 (pt) REVERT: f 86 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7429 (mm-30) REVERT: g 64 PHE cc_start: 0.8723 (t80) cc_final: 0.7878 (t80) REVERT: g 71 ASN cc_start: 0.8664 (m110) cc_final: 0.8252 (m-40) REVERT: g 100 ASN cc_start: 0.7751 (m-40) cc_final: 0.7341 (t0) outliers start: 126 outliers final: 52 residues processed: 573 average time/residue: 1.1366 time to fit residues: 805.1429 Evaluate side-chains 540 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 472 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 746 THR 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 B residue 91 ARG 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 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 225 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 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 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 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 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 389 HIS Chi-restraints excluded: chain a residue 396 ILE Chi-restraints excluded: chain a residue 440 LEU Chi-restraints excluded: chain a residue 594 PHE 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 a residue 792 ASP 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 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 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 161 LYS Chi-restraints excluded: chain d residue 169 SER Chi-restraints excluded: chain d residue 446 LEU 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 145 ILE 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 13 VAL 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 165 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 258 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 268 optimal weight: 5.9990 chunk 357 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 161 optimal weight: 9.9990 chunk 208 optimal weight: 3.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.142553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115591 restraints weight = 43447.342| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.92 r_work: 0.3319 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30962 Z= 0.191 Angle : 0.691 11.432 41942 Z= 0.351 Chirality : 0.045 0.373 4988 Planarity : 0.005 0.060 4948 Dihedral : 12.772 168.581 4806 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.45 % Allowed : 15.95 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3716 helix: 1.70 (0.10), residues: 2750 sheet: -0.25 (0.57), residues: 94 loop : -2.76 (0.18), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 298 HIS 0.009 0.001 HIS D 272 PHE 0.030 0.002 PHE A 376 TYR 0.022 0.002 TYR a 466 ARG 0.007 0.001 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.06210 ( 2167) hydrogen bonds : angle 4.14627 ( 6459) covalent geometry : bond 0.00448 (30962) covalent geometry : angle 0.69098 (41942) *********************** 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 605 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 497 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.8075 (m) cc_final: 0.7598 (p) REVERT: A 123 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8792 (tm) REVERT: A 131 LYS cc_start: 0.6365 (ttpp) cc_final: 0.5900 (tttt) REVERT: A 277 MET cc_start: 0.7862 (tpt) cc_final: 0.7061 (tpt) REVERT: A 440 LEU cc_start: 0.7880 (mt) cc_final: 0.7648 (tm) REVERT: A 568 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.6757 (mpt-90) REVERT: A 688 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8596 (tt) REVERT: A 701 THR cc_start: 0.8600 (p) cc_final: 0.8300 (m) REVERT: A 722 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7011 (mmtm) REVERT: B 18 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8252 (tp) REVERT: C 60 LYS cc_start: 0.7214 (mttt) cc_final: 0.6660 (ttpp) REVERT: C 63 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8215 (ptm-80) REVERT: D 5 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7887 (tt) REVERT: D 229 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.7955 (tt) REVERT: D 293 TYR cc_start: 0.8221 (m-80) cc_final: 0.7856 (m-80) REVERT: D 461 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8454 (mp) REVERT: E 67 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7266 (tp30) REVERT: E 108 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8225 (tmm) REVERT: E 110 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7292 (pt) REVERT: E 119 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7723 (pp) REVERT: E 157 SER cc_start: 0.6993 (t) cc_final: 0.6634 (m) REVERT: a 48 PHE cc_start: 0.6931 (t80) cc_final: 0.6597 (t80) REVERT: a 440 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7632 (tm) REVERT: a 495 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6672 (tpp) REVERT: a 568 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.6931 (mpt-90) REVERT: a 701 THR cc_start: 0.8756 (p) cc_final: 0.8503 (m) REVERT: a 722 LYS cc_start: 0.8177 (mmpt) cc_final: 0.7285 (mmtm) REVERT: b 62 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8034 (ttpp) REVERT: b 78 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.7302 (t80) REVERT: c 5 MET cc_start: 0.8385 (mmm) cc_final: 0.8140 (mmm) REVERT: c 60 LYS cc_start: 0.7473 (mttt) cc_final: 0.6944 (ttpp) REVERT: c 63 ARG cc_start: 0.8718 (ptm160) cc_final: 0.8259 (ptm-80) REVERT: d 5 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7844 (tt) REVERT: d 293 TYR cc_start: 0.8167 (m-80) cc_final: 0.7933 (m-80) REVERT: d 405 ILE cc_start: 0.8620 (mm) cc_final: 0.8367 (mt) REVERT: e 102 GLU cc_start: 0.7307 (pt0) cc_final: 0.7011 (pt0) REVERT: e 108 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8042 (tmm) REVERT: e 110 ILE cc_start: 0.7866 (OUTLIER) cc_final: 0.7414 (pt) REVERT: f 86 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7380 (mm-30) REVERT: g 71 ASN cc_start: 0.8699 (m110) cc_final: 0.8234 (m-40) REVERT: g 100 ASN cc_start: 0.7743 (m-40) cc_final: 0.7286 (t0) outliers start: 108 outliers final: 55 residues processed: 559 average time/residue: 1.2487 time to fit residues: 859.3416 Evaluate side-chains 544 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 472 time to evaluate : 4.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 62 LYS Chi-restraints excluded: chain B residue 91 ARG 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 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain D residue 455 LEU 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 67 GLU 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 119 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 3 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 120 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 194 MET Chi-restraints excluded: chain a residue 258 LEU Chi-restraints excluded: chain a residue 389 HIS Chi-restraints excluded: chain a residue 396 ILE 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 62 LYS Chi-restraints excluded: chain b residue 78 PHE Chi-restraints excluded: chain b residue 85 SER 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 137 GLU Chi-restraints excluded: chain d residue 155 GLN Chi-restraints excluded: chain d residue 161 LYS Chi-restraints excluded: chain d residue 169 SER 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 153 ILE Chi-restraints excluded: chain e residue 157 SER Chi-restraints excluded: chain f residue 59 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 86 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 157 optimal weight: 20.0000 chunk 287 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 344 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 GLN d 354 ASN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN ** g 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.146422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.119759 restraints weight = 43107.341| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.92 r_work: 0.3373 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30962 Z= 0.140 Angle : 0.642 11.966 41942 Z= 0.325 Chirality : 0.043 0.368 4988 Planarity : 0.005 0.058 4948 Dihedral : 12.194 176.175 4806 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.03 % Allowed : 16.62 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.14), residues: 3716 helix: 1.93 (0.10), residues: 2762 sheet: -0.06 (0.58), residues: 94 loop : -2.70 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 298 HIS 0.004 0.001 HIS D 272 PHE 0.033 0.001 PHE A 376 TYR 0.027 0.001 TYR A 466 ARG 0.007 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.05310 ( 2167) hydrogen bonds : angle 3.97528 ( 6459) covalent geometry : bond 0.00301 (30962) covalent geometry : angle 0.64218 (41942) *********************** 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 615 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 520 time to evaluate : 5.777 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.8022 (m) cc_final: 0.7463 (p) REVERT: A 123 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8801 (tm) REVERT: A 131 LYS cc_start: 0.6389 (ttpp) cc_final: 0.5903 (tttt) REVERT: A 255 TYR cc_start: 0.8590 (p90) cc_final: 0.8363 (p90) REVERT: A 277 MET cc_start: 0.7854 (tpt) cc_final: 0.7402 (tpt) REVERT: A 440 LEU cc_start: 0.7898 (mt) cc_final: 0.7678 (tm) REVERT: A 516 LEU cc_start: 0.7674 (tp) cc_final: 0.7065 (mt) REVERT: A 568 ARG cc_start: 0.7986 (tpp-160) cc_final: 0.6719 (mpt-90) REVERT: A 688 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8591 (tt) REVERT: A 701 THR cc_start: 0.8612 (p) cc_final: 0.8255 (m) REVERT: A 722 LYS cc_start: 0.7978 (mmpt) cc_final: 0.7082 (mmtm) REVERT: B 18 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8179 (tp) REVERT: B 78 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6608 (t80) REVERT: C 60 LYS cc_start: 0.6988 (mttt) cc_final: 0.6508 (ttpp) REVERT: C 63 ARG cc_start: 0.8625 (ptm160) cc_final: 0.8166 (ptm-80) REVERT: D 293 TYR cc_start: 0.8168 (m-80) cc_final: 0.7855 (m-80) REVERT: D 318 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7066 (tpt) REVERT: D 461 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8431 (mp) REVERT: E 102 GLU cc_start: 0.7292 (pt0) cc_final: 0.6888 (pt0) REVERT: E 108 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7899 (tmm) REVERT: E 110 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7189 (pt) REVERT: E 157 SER cc_start: 0.6939 (t) cc_final: 0.6626 (m) REVERT: F 58 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7575 (mt) REVERT: G 94 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.7255 (ttp80) REVERT: a 48 PHE cc_start: 0.6991 (t80) cc_final: 0.6682 (t80) REVERT: a 440 LEU cc_start: 0.8241 (mm) cc_final: 0.7610 (tm) REVERT: a 495 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6853 (tpp) REVERT: a 568 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.6875 (mpt-90) REVERT: a 701 THR cc_start: 0.8710 (p) cc_final: 0.8476 (m) REVERT: a 722 LYS cc_start: 0.8184 (mmpt) cc_final: 0.7306 (mmtm) REVERT: b 78 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.7252 (t80) REVERT: b 87 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6391 (ptm) REVERT: c 5 MET cc_start: 0.8372 (mmm) cc_final: 0.8151 (mmm) REVERT: c 23 LYS cc_start: 0.7242 (tttt) cc_final: 0.6320 (tmmt) REVERT: c 60 LYS cc_start: 0.7319 (mttt) cc_final: 0.6836 (ttpp) REVERT: c 63 ARG cc_start: 0.8658 (ptm160) cc_final: 0.8205 (ptm-80) REVERT: d 5 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7895 (tt) REVERT: d 76 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (m) REVERT: d 109 TYR cc_start: 0.7848 (t80) cc_final: 0.7628 (t80) REVERT: d 293 TYR cc_start: 0.8182 (m-80) cc_final: 0.7963 (m-80) REVERT: d 295 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6952 (t70) REVERT: e 102 GLU cc_start: 0.7293 (pt0) cc_final: 0.6847 (pt0) REVERT: e 108 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8032 (tmm) REVERT: e 110 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7366 (pt) REVERT: f 86 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7339 (mm-30) REVERT: g 64 PHE cc_start: 0.8613 (t80) cc_final: 0.7998 (t80) REVERT: g 71 ASN cc_start: 0.8674 (m110) cc_final: 0.8199 (m-40) REVERT: g 100 ASN cc_start: 0.7721 (m-40) cc_final: 0.7226 (t0) outliers start: 95 outliers final: 47 residues processed: 567 average time/residue: 1.3360 time to fit residues: 940.3325 Evaluate side-chains 541 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 477 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG 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 688 LEU 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 78 PHE Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 225 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 461 ILE Chi-restraints excluded: chain D residue 476 VAL 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 19 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 72 SER 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 389 HIS Chi-restraints excluded: chain a residue 455 VAL Chi-restraints excluded: chain a residue 495 MET Chi-restraints excluded: chain a residue 509 ILE 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 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 87 MET Chi-restraints excluded: chain b residue 90 ASP 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 75 ASP Chi-restraints excluded: chain d residue 76 SER 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 99 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 234 optimal weight: 0.0010 chunk 63 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 342 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 96 GLN d 155 GLN ** e 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 53 ASN ** g 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.146594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120075 restraints weight = 43414.212| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.91 r_work: 0.3382 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2844 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= 0.143 Angle : 0.649 12.111 41942 Z= 0.327 Chirality : 0.043 0.370 4988 Planarity : 0.004 0.054 4948 Dihedral : 11.857 179.153 4806 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.97 % Allowed : 17.20 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.14), residues: 3716 helix: 1.98 (0.10), residues: 2780 sheet: 0.04 (0.59), residues: 94 loop : -2.74 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 298 HIS 0.005 0.001 HIS D 272 PHE 0.032 0.001 PHE A 376 TYR 0.027 0.001 TYR a 466 ARG 0.008 0.000 ARG A 394 Details of bonding type rmsd hydrogen bonds : bond 0.05263 ( 2167) hydrogen bonds : angle 3.94503 ( 6459) covalent geometry : bond 0.00312 (30962) covalent geometry : angle 0.64910 (41942) *********************** 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 596 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 503 time to evaluate : 3.218 Fit side-chains revert: symmetry clash REVERT: A 94 SER cc_start: 0.7973 (m) cc_final: 0.7430 (p) REVERT: A 123 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8801 (tm) REVERT: A 131 LYS cc_start: 0.6266 (ttpp) cc_final: 0.5886 (tttt) REVERT: A 277 MET cc_start: 0.7883 (tpt) cc_final: 0.7376 (tpt) REVERT: A 440 LEU cc_start: 0.7913 (mt) cc_final: 0.7679 (tm) REVERT: A 516 LEU cc_start: 0.7707 (tp) cc_final: 0.7133 (mt) REVERT: A 568 ARG cc_start: 0.7952 (tpp-160) cc_final: 0.6678 (mpt-90) REVERT: A 688 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 701 THR cc_start: 0.8597 (p) cc_final: 0.8263 (m) REVERT: A 722 LYS cc_start: 0.7956 (mmpt) cc_final: 0.7044 (mmtm) REVERT: B 18 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8168 (tp) REVERT: B 78 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6651 (t80) REVERT: C 11 CYS cc_start: 0.8399 (t) cc_final: 0.7723 (m) REVERT: C 60 LYS cc_start: 0.6928 (mttt) cc_final: 0.6431 (ttpp) REVERT: C 63 ARG cc_start: 0.8616 (ptm160) cc_final: 0.8149 (ptm-80) REVERT: D 137 GLU cc_start: 0.7709 (mp0) cc_final: 0.7476 (mp0) REVERT: D 197 ASN cc_start: 0.8332 (m-40) cc_final: 0.7963 (t0) REVERT: D 229 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7896 (tt) REVERT: D 293 TYR cc_start: 0.8162 (m-80) cc_final: 0.7875 (m-80) REVERT: D 318 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.7124 (tpt) REVERT: D 461 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8441 (mp) REVERT: E 108 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7793 (tmm) REVERT: E 110 ILE cc_start: 0.7558 (OUTLIER) cc_final: 0.7211 (pt) REVERT: E 142 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7124 (tp) REVERT: E 157 SER cc_start: 0.6962 (t) cc_final: 0.6647 (m) REVERT: F 58 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7545 (mt) REVERT: G 94 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7304 (ttp80) REVERT: a 48 PHE cc_start: 0.6972 (t80) cc_final: 0.6662 (t80) REVERT: a 143 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8648 (tt) REVERT: a 440 LEU cc_start: 0.8265 (mm) cc_final: 0.7609 (tm) REVERT: a 568 ARG cc_start: 0.8062 (tpp-160) cc_final: 0.6892 (mpt-90) REVERT: a 603 SER cc_start: 0.8029 (m) cc_final: 0.7444 (p) REVERT: a 701 THR cc_start: 0.8681 (p) cc_final: 0.8459 (m) REVERT: a 722 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7261 (mmtt) REVERT: b 78 PHE cc_start: 0.7547 (OUTLIER) cc_final: 0.7315 (t80) REVERT: b 87 MET cc_start: 0.6715 (ptp) cc_final: 0.6413 (ptm) REVERT: c 11 CYS cc_start: 0.8581 (t) cc_final: 0.7817 (m) REVERT: c 23 LYS cc_start: 0.7230 (tttt) cc_final: 0.6416 (tmmt) REVERT: c 24 SER cc_start: 0.6464 (OUTLIER) cc_final: 0.6201 (m) REVERT: c 60 LYS cc_start: 0.7285 (mttt) cc_final: 0.6822 (ttpp) REVERT: c 63 ARG cc_start: 0.8641 (ptm160) cc_final: 0.8163 (ptm-80) REVERT: c 101 ASP cc_start: 0.7360 (t0) cc_final: 0.7091 (t0) REVERT: d 5 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7948 (tt) REVERT: d 76 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7893 (m) REVERT: d 109 TYR cc_start: 0.7877 (t80) cc_final: 0.7670 (t80) REVERT: d 189 MET cc_start: 0.8329 (mtt) cc_final: 0.8118 (mtt) REVERT: d 293 TYR cc_start: 0.8156 (m-80) cc_final: 0.7861 (m-80) REVERT: e 102 GLU cc_start: 0.7327 (pt0) cc_final: 0.6612 (pt0) REVERT: e 108 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8079 (tmm) REVERT: e 110 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7373 (pt) REVERT: f 86 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7310 (mm-30) REVERT: g 64 PHE cc_start: 0.8647 (t80) cc_final: 0.7982 (t80) REVERT: g 71 ASN cc_start: 0.8664 (m110) cc_final: 0.8217 (m-40) REVERT: g 100 ASN cc_start: 0.7697 (m-40) cc_final: 0.7217 (t0) outliers start: 93 outliers final: 46 residues processed: 555 average time/residue: 1.1087 time to fit residues: 756.6081 Evaluate side-chains 546 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 482 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG 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 667 VAL Chi-restraints excluded: chain A residue 688 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 B residue 91 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 455 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 476 VAL 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 121 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 142 ILE Chi-restraints excluded: chain F residue 58 LEU 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 33 ILE 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 389 HIS 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 b residue 90 ASP 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 75 ASP Chi-restraints excluded: chain d residue 76 SER 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 153 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.4569 > 50: distance: 35 - 43: 23.853 distance: 43 - 44: 41.924 distance: 44 - 45: 4.789 distance: 45 - 46: 34.866 distance: 45 - 47: 56.984 distance: 47 - 48: 31.306 distance: 48 - 49: 37.755 distance: 48 - 51: 40.114 distance: 49 - 50: 11.741 distance: 49 - 58: 48.231 distance: 52 - 53: 49.173 distance: 52 - 54: 39.544 distance: 53 - 55: 42.081 distance: 55 - 57: 5.721 distance: 56 - 57: 40.793 distance: 58 - 59: 55.967 distance: 59 - 60: 26.691 distance: 59 - 62: 55.217 distance: 60 - 61: 37.350 distance: 60 - 65: 35.196 distance: 62 - 63: 28.694 distance: 62 - 64: 25.201 distance: 65 - 66: 39.203 distance: 65 - 71: 20.621 distance: 66 - 69: 39.292 distance: 67 - 72: 56.778 distance: 69 - 70: 24.336 distance: 70 - 71: 30.069 distance: 73 - 74: 30.956 distance: 73 - 76: 40.384 distance: 74 - 75: 18.402 distance: 74 - 81: 40.763 distance: 75 - 108: 51.533 distance: 77 - 78: 10.705 distance: 78 - 79: 9.308 distance: 78 - 80: 51.400 distance: 81 - 82: 32.567 distance: 82 - 83: 10.752 distance: 82 - 85: 44.600 distance: 83 - 84: 5.233 distance: 83 - 89: 14.978 distance: 84 - 115: 56.063 distance: 85 - 86: 29.822 distance: 86 - 87: 16.090 distance: 89 - 90: 3.494 distance: 90 - 91: 10.536 distance: 90 - 93: 5.442 distance: 91 - 100: 41.116 distance: 92 - 123: 26.180 distance: 93 - 94: 12.045 distance: 94 - 95: 50.620 distance: 94 - 96: 29.601 distance: 95 - 97: 28.869 distance: 96 - 98: 21.723 distance: 97 - 99: 13.231 distance: 98 - 99: 21.197 distance: 100 - 101: 27.106 distance: 101 - 102: 34.681 distance: 101 - 104: 42.447 distance: 102 - 103: 28.231 distance: 102 - 108: 30.218 distance: 103 - 127: 30.584 distance: 104 - 105: 17.545 distance: 106 - 107: 34.398 distance: 108 - 109: 46.662 distance: 109 - 110: 30.645 distance: 109 - 112: 7.873 distance: 110 - 111: 44.320 distance: 111 - 134: 30.316 distance: 112 - 114: 21.844 distance: 115 - 116: 34.640 distance: 116 - 117: 35.515 distance: 116 - 119: 39.613 distance: 117 - 118: 7.418 distance: 117 - 123: 31.466 distance: 118 - 140: 38.019 distance: 119 - 120: 56.822 distance: 119 - 121: 42.841 distance: 120 - 122: 43.303