Starting phenix.real_space_refine on Fri May 23 16:52:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eow_28487/05_2025/8eow_28487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eow_28487/05_2025/8eow_28487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eow_28487/05_2025/8eow_28487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eow_28487/05_2025/8eow_28487.map" model { file = "/net/cci-nas-00/data/ceres_data/8eow_28487/05_2025/8eow_28487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eow_28487/05_2025/8eow_28487.cif" } resolution = 3.9 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= 0.004 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15892 2.51 5 N 4116 2.21 5 O 4492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24628 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "E" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "D" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "C" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "B" Number of atoms: 5275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5275 Classifications: {'peptide': 701} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 401 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'GLU%COO:plan': 1, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 239 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "F" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 882 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Time building chain proxies: 14.82, per 1000 atoms: 0.60 Number of scatterers: 24628 At special positions: 0 Unit cell: (165.24, 165.24, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4492 8.00 N 4116 7.00 C 15892 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: 6.70 Conformation dependent library (CDL) restraints added in 3.6 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 65.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 16 through 26 removed outlier: 4.231A pdb=" N ASN A 26 " --> pdb=" O VAL A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 76 through 90 Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.745A pdb=" N LYS A 137 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 175 through 189 removed outlier: 3.812A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.008A pdb=" N ASP A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 241 removed outlier: 3.683A pdb=" N TRP A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 223 " --> pdb=" O THR A 219 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 268 removed outlier: 3.536A pdb=" N VAL A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 removed outlier: 3.913A pdb=" N ARG A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N MET A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 305 through 314 removed outlier: 3.910A pdb=" N ILE A 309 " --> pdb=" O PRO A 305 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 325 Processing helix chain 'A' and resid 326 through 333 removed outlier: 3.651A pdb=" N LEU A 332 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 333 " --> pdb=" O ARG A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 345 removed outlier: 4.715A pdb=" N ASP A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N HIS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N TYR A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 379 removed outlier: 3.761A pdb=" N VAL A 351 " --> pdb=" O TYR A 347 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE A 379 " --> pdb=" O ASP A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 390 through 400 removed outlier: 3.796A pdb=" N ALA A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 436 removed outlier: 3.644A pdb=" N ILE A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 499 removed outlier: 5.304A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 521 removed outlier: 4.501A pdb=" N ARG A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 532 removed outlier: 3.762A pdb=" N CYS A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 545 Processing helix chain 'A' and resid 545 through 552 removed outlier: 3.733A pdb=" N GLU A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 556 Processing helix chain 'A' and resid 559 through 570 removed outlier: 4.014A pdb=" N GLU A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 Processing helix chain 'A' and resid 647 through 657 Processing helix chain 'A' and resid 657 through 668 removed outlier: 3.783A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG A 666 " --> pdb=" O HIS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 695 Processing helix chain 'A' and resid 707 through 722 Processing helix chain 'E' and resid 7 through 10 removed outlier: 3.593A pdb=" N ALA E 10 " --> pdb=" O GLU E 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 7 through 10' Processing helix chain 'E' and resid 11 through 20 removed outlier: 4.247A pdb=" N ALA E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.627A pdb=" N PHE E 68 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS E 77 " --> pdb=" O ALA E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 101 through 113 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 147 removed outlier: 3.773A pdb=" N ALA E 147 " --> pdb=" O GLN E 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 26 removed outlier: 4.231A pdb=" N ASN D 26 " --> pdb=" O VAL D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 76 through 90 Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.736A pdb=" N LYS D 137 " --> pdb=" O THR D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.809A pdb=" N LYS D 180 " --> pdb=" O GLU D 176 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS D 181 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL D 187 " --> pdb=" O ARG D 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.006A pdb=" N ASP D 193 " --> pdb=" O GLN D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 241 removed outlier: 3.678A pdb=" N TRP D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE D 223 " --> pdb=" O THR D 219 " (cutoff:3.500A) Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 248 through 268 removed outlier: 3.530A pdb=" N VAL D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 295 removed outlier: 3.921A pdb=" N ARG D 288 " --> pdb=" O PRO D 284 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N MET D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 303 Processing helix chain 'D' and resid 305 through 314 removed outlier: 3.910A pdb=" N ILE D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN D 310 " --> pdb=" O TYR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 325 Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.644A pdb=" N LEU D 332 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 333 " --> pdb=" O ARG D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 345 removed outlier: 4.812A pdb=" N ASP D 342 " --> pdb=" O ALA D 338 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N HIS D 343 " --> pdb=" O ARG D 339 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 379 removed outlier: 3.744A pdb=" N VAL D 351 " --> pdb=" O TYR D 347 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE D 379 " --> pdb=" O ASP D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 390 through 400 removed outlier: 3.845A pdb=" N ALA D 396 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 436 removed outlier: 3.646A pdb=" N ILE D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 499 removed outlier: 5.301A pdb=" N ASN D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR D 482 " --> pdb=" O MET D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 521 removed outlier: 4.522A pdb=" N ARG D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 532 removed outlier: 3.765A pdb=" N CYS D 532 " --> pdb=" O VAL D 528 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 545 Processing helix chain 'D' and resid 545 through 552 removed outlier: 3.734A pdb=" N GLU D 551 " --> pdb=" O LYS D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 556 Processing helix chain 'D' and resid 559 through 568 Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 647 through 657 Processing helix chain 'D' and resid 657 through 668 removed outlier: 3.779A pdb=" N SER D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG D 666 " --> pdb=" O HIS D 662 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 695 Processing helix chain 'D' and resid 707 through 722 Processing helix chain 'C' and resid 16 through 26 removed outlier: 4.233A pdb=" N ASN C 26 " --> pdb=" O VAL C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 67 through 71 Processing helix chain 'C' and resid 76 through 90 Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.727A pdb=" N LYS C 137 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 175 through 189 removed outlier: 3.809A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 removed outlier: 4.005A pdb=" N ASP C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 241 removed outlier: 3.677A pdb=" N TRP C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 223 " --> pdb=" O THR C 219 " (cutoff:3.500A) Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 268 removed outlier: 3.530A pdb=" N VAL C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 removed outlier: 3.926A pdb=" N ARG C 288 " --> pdb=" O PRO C 284 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 305 through 314 removed outlier: 3.911A pdb=" N ILE C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASN C 310 " --> pdb=" O TYR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 325 Processing helix chain 'C' and resid 326 through 333 removed outlier: 3.628A pdb=" N LEU C 332 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 333 " --> pdb=" O ARG C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 345 removed outlier: 4.820A pdb=" N ASP C 342 " --> pdb=" O ALA C 338 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N HIS C 343 " --> pdb=" O ARG C 339 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 379 removed outlier: 3.748A pdb=" N VAL C 351 " --> pdb=" O TYR C 347 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU C 352 " --> pdb=" O GLY C 348 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE C 379 " --> pdb=" O ASP C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 390 through 400 removed outlier: 3.860A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY C 400 " --> pdb=" O ALA C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 436 removed outlier: 3.647A pdb=" N ILE C 424 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 499 removed outlier: 5.300A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 521 removed outlier: 4.499A pdb=" N ARG C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 532 removed outlier: 3.767A pdb=" N CYS C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 545 Processing helix chain 'C' and resid 545 through 552 removed outlier: 3.739A pdb=" N GLU C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 559 through 568 Processing helix chain 'C' and resid 620 through 625 Processing helix chain 'C' and resid 647 through 657 Processing helix chain 'C' and resid 657 through 668 removed outlier: 3.764A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 666 " --> pdb=" O HIS C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 695 Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'B' and resid 16 through 26 removed outlier: 4.239A pdb=" N ASN B 26 " --> pdb=" O VAL B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 76 through 90 Processing helix chain 'B' and resid 133 through 137 removed outlier: 3.738A pdb=" N LYS B 137 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 156 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.810A pdb=" N LYS B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N HIS B 181 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 187 " --> pdb=" O ARG B 183 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 194 removed outlier: 4.011A pdb=" N ASP B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 241 removed outlier: 3.726A pdb=" N TRP B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 248 through 268 removed outlier: 3.535A pdb=" N VAL B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 removed outlier: 3.925A pdb=" N ARG B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N MET B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 305 through 314 removed outlier: 3.896A pdb=" N ILE B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN B 310 " --> pdb=" O TYR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 325 Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.705A pdb=" N LEU B 332 " --> pdb=" O VAL B 329 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG B 333 " --> pdb=" O ARG B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 345 removed outlier: 4.794A pdb=" N ASP B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N HIS B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 379 removed outlier: 3.790A pdb=" N VAL B 351 " --> pdb=" O TYR B 347 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 379 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 390 through 400 removed outlier: 3.869A pdb=" N ALA B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 436 removed outlier: 3.615A pdb=" N ILE B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 499 removed outlier: 5.301A pdb=" N ASN B 481 " --> pdb=" O GLN B 477 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR B 482 " --> pdb=" O MET B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 521 removed outlier: 4.497A pdb=" N ARG B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 532 removed outlier: 3.768A pdb=" N CYS B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 545 Processing helix chain 'B' and resid 545 through 552 removed outlier: 3.739A pdb=" N GLU B 551 " --> pdb=" O LYS B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 Processing helix chain 'B' and resid 559 through 568 Processing helix chain 'B' and resid 620 through 625 Processing helix chain 'B' and resid 647 through 657 Processing helix chain 'B' and resid 657 through 668 removed outlier: 3.724A pdb=" N SER B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG B 666 " --> pdb=" O HIS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 695 Processing helix chain 'B' and resid 707 through 722 Processing helix chain 'H' and resid 7 through 10 removed outlier: 3.571A pdb=" N ALA H 10 " --> pdb=" O GLU H 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 7 through 10' Processing helix chain 'H' and resid 11 through 20 removed outlier: 4.233A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 Processing helix chain 'H' and resid 44 through 56 Processing helix chain 'H' and resid 64 through 77 removed outlier: 3.612A pdb=" N PHE H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS H 77 " --> pdb=" O ALA H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.867A pdb=" N ALA H 147 " --> pdb=" O GLN H 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 10 removed outlier: 3.568A pdb=" N ALA G 10 " --> pdb=" O GLU G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 7 through 10' Processing helix chain 'G' and resid 11 through 20 removed outlier: 4.254A pdb=" N ALA G 15 " --> pdb=" O GLU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 40 Processing helix chain 'G' and resid 44 through 56 Processing helix chain 'G' and resid 64 through 77 removed outlier: 3.623A pdb=" N PHE G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS G 77 " --> pdb=" O ALA G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 147 removed outlier: 3.712A pdb=" N ALA G 147 " --> pdb=" O GLN G 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 10 removed outlier: 3.566A pdb=" N ALA F 10 " --> pdb=" O GLU F 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 7 through 10' Processing helix chain 'F' and resid 11 through 20 removed outlier: 4.275A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 40 Processing helix chain 'F' and resid 44 through 56 Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.568A pdb=" N PHE F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS F 77 " --> pdb=" O ALA F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 117 through 129 removed outlier: 3.625A pdb=" N ALA F 128 " --> pdb=" O MET F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.772A pdb=" N ALA F 147 " --> pdb=" O GLN F 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.582A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 6.582A pdb=" N LEU A 32 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 571 through 575 removed outlier: 3.501A pdb=" N CYS A 640 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP A 641 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS A 592 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 617 " --> pdb=" O CYS A 592 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 672 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 618 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 587 through 588 removed outlier: 4.826A pdb=" N ALA A 628 " --> pdb=" O VAL A 588 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 607 through 611 removed outlier: 4.125A pdb=" N ALA A 609 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU D 32 " --> pdb=" O VAL D 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU D 32 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D 125 " --> pdb=" O ILE D 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 99 through 100 Processing sheet with id=AB1, first strand: chain 'D' and resid 571 through 575 removed outlier: 6.434A pdb=" N ASP D 641 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS D 592 " --> pdb=" O PHE D 617 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE D 617 " --> pdb=" O CYS D 592 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP D 615 " --> pdb=" O VAL D 594 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR D 672 " --> pdb=" O VAL D 616 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY D 618 " --> pdb=" O TYR D 672 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 587 through 588 removed outlier: 4.826A pdb=" N ALA D 628 " --> pdb=" O VAL D 588 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 607 through 611 removed outlier: 4.114A pdb=" N ALA D 609 " --> pdb=" O VAL D 601 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 42 through 44 removed outlier: 6.603A pdb=" N LEU C 32 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AB7, first strand: chain 'C' and resid 571 through 575 removed outlier: 3.500A pdb=" N CYS C 640 " --> pdb=" O CYS C 575 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP C 641 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N CYS C 592 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 617 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR C 672 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 618 " --> pdb=" O TYR C 672 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 587 through 588 removed outlier: 4.838A pdb=" N ALA C 628 " --> pdb=" O VAL C 588 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 607 through 611 removed outlier: 4.125A pdb=" N ALA C 609 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 44 removed outlier: 6.601A pdb=" N LEU B 32 " --> pdb=" O VAL B 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 42 through 44 removed outlier: 6.601A pdb=" N LEU B 32 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B 125 " --> pdb=" O ILE B 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 99 through 100 Processing sheet with id=AC4, first strand: chain 'B' and resid 571 through 575 removed outlier: 3.500A pdb=" N CYS B 640 " --> pdb=" O CYS B 575 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ASP B 641 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N CYS B 592 " --> pdb=" O PHE B 617 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 617 " --> pdb=" O CYS B 592 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP B 615 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR B 672 " --> pdb=" O VAL B 616 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 618 " --> pdb=" O TYR B 672 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 587 through 588 removed outlier: 4.808A pdb=" N ALA B 628 " --> pdb=" O VAL B 588 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 607 through 611 removed outlier: 4.132A pdb=" N ALA B 609 " --> pdb=" O VAL B 601 " (cutoff:3.500A) 1505 hydrogen bonds defined for protein. 4332 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: 8.79 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8020 1.34 - 1.46: 6091 1.46 - 1.58: 10881 1.58 - 1.70: 0 1.70 - 1.81: 196 Bond restraints: 25188 Sorted by residual: bond pdb=" CG1 ILE D 456 " pdb=" CD1 ILE D 456 " ideal model delta sigma weight residual 1.513 1.475 0.038 3.90e-02 6.57e+02 9.36e-01 bond pdb=" CG1 ILE A 456 " pdb=" CD1 ILE A 456 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.82e-01 bond pdb=" CG1 ILE B 456 " pdb=" CD1 ILE B 456 " ideal model delta sigma weight residual 1.513 1.476 0.037 3.90e-02 6.57e+02 8.80e-01 bond pdb=" CG1 ILE C 456 " pdb=" CD1 ILE C 456 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.75e-01 bond pdb=" CB ASP C 254 " pdb=" CG ASP C 254 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.31e-01 ... (remaining 25183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 33965 1.96 - 3.91: 384 3.91 - 5.87: 63 5.87 - 7.82: 24 7.82 - 9.78: 8 Bond angle restraints: 34444 Sorted by residual: angle pdb=" CA LEU A 331 " pdb=" CB LEU A 331 " pdb=" CG LEU A 331 " ideal model delta sigma weight residual 116.30 126.08 -9.78 3.50e+00 8.16e-02 7.80e+00 angle pdb=" CB MET F 144 " pdb=" CG MET F 144 " pdb=" SD MET F 144 " ideal model delta sigma weight residual 112.70 121.04 -8.34 3.00e+00 1.11e-01 7.73e+00 angle pdb=" CA LEU C 331 " pdb=" CB LEU C 331 " pdb=" CG LEU C 331 " ideal model delta sigma weight residual 116.30 125.96 -9.66 3.50e+00 8.16e-02 7.62e+00 angle pdb=" CA LEU B 292 " pdb=" CB LEU B 292 " pdb=" CG LEU B 292 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 angle pdb=" CA LEU B 331 " pdb=" CB LEU B 331 " pdb=" CG LEU B 331 " ideal model delta sigma weight residual 116.30 125.88 -9.58 3.50e+00 8.16e-02 7.50e+00 ... (remaining 34439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12699 17.11 - 34.22: 1506 34.22 - 51.33: 359 51.33 - 68.44: 49 68.44 - 85.55: 27 Dihedral angle restraints: 14640 sinusoidal: 4764 harmonic: 9876 Sorted by residual: dihedral pdb=" CA GLU C 377 " pdb=" C GLU C 377 " pdb=" N ILE C 378 " pdb=" CA ILE C 378 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU D 377 " pdb=" C GLU D 377 " pdb=" N ILE D 378 " pdb=" CA ILE D 378 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU A 377 " pdb=" C GLU A 377 " pdb=" N ILE A 378 " pdb=" CA ILE A 378 " ideal model delta harmonic sigma weight residual 180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 14637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2300 0.027 - 0.053: 1087 0.053 - 0.080: 404 0.080 - 0.106: 189 0.106 - 0.133: 72 Chirality restraints: 4052 Sorted by residual: chirality pdb=" CA ILE B 442 " pdb=" N ILE B 442 " pdb=" C ILE B 442 " pdb=" CB ILE B 442 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE A 442 " pdb=" N ILE A 442 " pdb=" C ILE A 442 " pdb=" CB ILE A 442 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE D 442 " pdb=" N ILE D 442 " pdb=" C ILE D 442 " pdb=" CB ILE D 442 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 4049 not shown) Planarity restraints: 4420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 704 " 0.037 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO C 705 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 705 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 705 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 704 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.75e+00 pdb=" N PRO B 705 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 705 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 705 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 704 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO A 705 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 705 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 705 " -0.030 5.00e-02 4.00e+02 ... (remaining 4417 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3115 2.75 - 3.29: 25000 3.29 - 3.82: 41242 3.82 - 4.36: 40702 4.36 - 4.90: 73545 Nonbonded interactions: 183604 Sorted by model distance: nonbonded pdb=" O ASN A 290 " pdb=" OG1 THR A 294 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR B 582 " pdb=" OG SER B 590 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR A 582 " pdb=" OG SER A 590 " model vdw 2.216 3.040 nonbonded pdb=" O ASN D 290 " pdb=" OG1 THR D 294 " model vdw 2.216 3.040 nonbonded pdb=" O ASN C 290 " pdb=" OG1 THR C 294 " model vdw 2.216 3.040 ... (remaining 183599 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.220 Process input model: 56.230 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 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 : 0.003 0.038 25188 Z= 0.126 Angle : 0.573 9.777 34444 Z= 0.296 Chirality : 0.039 0.133 4052 Planarity : 0.003 0.055 4420 Dihedral : 16.053 85.545 8240 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.35 % Allowed : 30.03 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.15), residues: 3340 helix: 1.98 (0.13), residues: 1932 sheet: -0.99 (0.34), residues: 208 loop : -0.30 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 295 HIS 0.006 0.001 HIS B 364 PHE 0.010 0.001 PHE A 429 TYR 0.016 0.001 TYR C 371 ARG 0.008 0.000 ARG D 677 Details of bonding type rmsd hydrogen bonds : bond 0.11266 ( 1485) hydrogen bonds : angle 4.64289 ( 4332) covalent geometry : bond 0.00272 (25188) covalent geometry : angle 0.57272 (34444) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 403 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 529 LEU cc_start: 0.7705 (tt) cc_final: 0.7257 (mm) REVERT: E 12 PHE cc_start: 0.6472 (t80) cc_final: 0.6121 (m-10) REVERT: E 136 VAL cc_start: 0.7633 (t) cc_final: 0.7266 (t) REVERT: D 529 LEU cc_start: 0.7730 (tt) cc_final: 0.7203 (mm) REVERT: C 529 LEU cc_start: 0.7684 (tt) cc_final: 0.7152 (mm) REVERT: B 292 LEU cc_start: 0.8164 (tt) cc_final: 0.7427 (mt) REVERT: H 12 PHE cc_start: 0.6489 (t80) cc_final: 0.6147 (m-10) REVERT: G 12 PHE cc_start: 0.6510 (t80) cc_final: 0.6133 (m-10) REVERT: G 105 LEU cc_start: 0.8069 (tp) cc_final: 0.7830 (tt) REVERT: F 12 PHE cc_start: 0.6482 (t80) cc_final: 0.5927 (m-10) REVERT: F 105 LEU cc_start: 0.7971 (tp) cc_final: 0.7761 (tt) outliers start: 8 outliers final: 8 residues processed: 409 average time/residue: 0.2897 time to fit residues: 199.2804 Evaluate side-chains 390 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 382 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 570 PHE Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 447 ASP Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain H residue 92 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 141 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 171 optimal weight: 40.0000 chunk 136 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 chunk 160 optimal weight: 9.9990 chunk 196 optimal weight: 0.0470 chunk 305 optimal weight: 9.9990 overall best weight: 4.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 583 HIS D 56 HIS D 583 HIS C 56 HIS C 583 HIS B 56 HIS B 290 ASN B 583 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.217698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.183806 restraints weight = 36747.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.183875 restraints weight = 84711.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.185074 restraints weight = 59861.684| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 25188 Z= 0.265 Angle : 0.670 8.948 34444 Z= 0.357 Chirality : 0.045 0.149 4052 Planarity : 0.004 0.053 4420 Dihedral : 4.658 53.591 3604 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.12 % Allowed : 27.84 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.82 (0.15), residues: 3340 helix: 1.46 (0.12), residues: 1936 sheet: -0.90 (0.34), residues: 208 loop : -0.64 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 222 HIS 0.013 0.002 HIS B 364 PHE 0.018 0.002 PHE B 664 TYR 0.021 0.002 TYR B 423 ARG 0.005 0.001 ARG D 677 Details of bonding type rmsd hydrogen bonds : bond 0.05665 ( 1485) hydrogen bonds : angle 4.27729 ( 4332) covalent geometry : bond 0.00634 (25188) covalent geometry : angle 0.67001 (34444) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 387 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8240 (tm-30) REVERT: E 12 PHE cc_start: 0.6498 (t80) cc_final: 0.6087 (m-10) REVERT: E 139 GLU cc_start: 0.7706 (mp0) cc_final: 0.7435 (mp0) REVERT: D 476 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 476 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8240 (tm-30) REVERT: B 476 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8261 (tm-30) REVERT: H 12 PHE cc_start: 0.6548 (t80) cc_final: 0.6094 (m-10) REVERT: H 92 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.6573 (t80) REVERT: H 141 PHE cc_start: 0.8140 (t80) cc_final: 0.7911 (t80) REVERT: G 12 PHE cc_start: 0.6526 (t80) cc_final: 0.6054 (m-10) REVERT: G 92 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6410 (t80) REVERT: G 141 PHE cc_start: 0.8320 (t80) cc_final: 0.8090 (t80) REVERT: F 12 PHE cc_start: 0.6503 (t80) cc_final: 0.5950 (m-10) REVERT: F 92 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6839 (t80) REVERT: F 141 PHE cc_start: 0.8076 (t80) cc_final: 0.7826 (t80) outliers start: 140 outliers final: 79 residues processed: 492 average time/residue: 0.2882 time to fit residues: 241.7844 Evaluate side-chains 453 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 371 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 482 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 492 VAL Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 482 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 130 ILE Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 145 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 263 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 309 optimal weight: 40.0000 chunk 157 optimal weight: 0.0980 chunk 170 optimal weight: 0.0000 chunk 106 optimal weight: 0.0570 chunk 293 optimal weight: 40.0000 chunk 158 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 222 optimal weight: 3.9990 overall best weight: 1.2306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.225998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.191647 restraints weight = 36172.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.190984 restraints weight = 79157.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.192723 restraints weight = 59047.026| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25188 Z= 0.122 Angle : 0.530 7.135 34444 Z= 0.278 Chirality : 0.040 0.156 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.968 51.514 3590 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.41 % Allowed : 30.03 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.15), residues: 3340 helix: 1.78 (0.13), residues: 1936 sheet: -0.58 (0.32), residues: 212 loop : -0.49 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 222 HIS 0.004 0.001 HIS C 364 PHE 0.014 0.001 PHE B 429 TYR 0.017 0.001 TYR C 371 ARG 0.003 0.000 ARG D 677 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1485) hydrogen bonds : angle 3.82169 ( 4332) covalent geometry : bond 0.00268 (25188) covalent geometry : angle 0.52978 (34444) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 397 time to evaluate : 2.693 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6620 (p90) REVERT: E 12 PHE cc_start: 0.6480 (t80) cc_final: 0.6075 (m-10) REVERT: E 92 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6510 (t80) REVERT: E 139 GLU cc_start: 0.7704 (mp0) cc_final: 0.7500 (mp0) REVERT: E 140 GLU cc_start: 0.5947 (mt-10) cc_final: 0.5607 (mt-10) REVERT: D 213 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6579 (p90) REVERT: C 213 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6580 (p90) REVERT: B 213 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6560 (p90) REVERT: H 12 PHE cc_start: 0.6430 (t80) cc_final: 0.6051 (m-10) REVERT: H 92 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6497 (t80) REVERT: G 12 PHE cc_start: 0.6494 (t80) cc_final: 0.6086 (m-10) REVERT: G 92 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6435 (t80) REVERT: G 141 PHE cc_start: 0.8368 (t80) cc_final: 0.8158 (t80) REVERT: F 12 PHE cc_start: 0.6473 (t80) cc_final: 0.5918 (m-10) REVERT: F 92 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6681 (t80) REVERT: F 141 PHE cc_start: 0.8267 (t80) cc_final: 0.7985 (t80) outliers start: 101 outliers final: 56 residues processed: 474 average time/residue: 0.2820 time to fit residues: 226.0115 Evaluate side-chains 443 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 379 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 145 MET Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 163 optimal weight: 20.0000 chunk 73 optimal weight: 0.0980 chunk 121 optimal weight: 0.0270 chunk 187 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 193 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 overall best weight: 2.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.222931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.188961 restraints weight = 36680.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.189720 restraints weight = 81576.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.190877 restraints weight = 50795.362| |-----------------------------------------------------------------------------| r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25188 Z= 0.153 Angle : 0.559 7.340 34444 Z= 0.293 Chirality : 0.041 0.171 4052 Planarity : 0.003 0.054 4420 Dihedral : 3.968 52.995 3590 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.42 % Allowed : 29.72 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.20 (0.15), residues: 3340 helix: 1.76 (0.13), residues: 1932 sheet: -0.43 (0.31), residues: 212 loop : -0.53 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 517 HIS 0.008 0.001 HIS C 364 PHE 0.013 0.001 PHE B 617 TYR 0.014 0.001 TYR B 423 ARG 0.003 0.000 ARG D 677 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 1485) hydrogen bonds : angle 3.84044 ( 4332) covalent geometry : bond 0.00361 (25188) covalent geometry : angle 0.55866 (34444) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 394 time to evaluate : 2.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6691 (p90) REVERT: A 434 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7922 (mt) REVERT: A 476 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8204 (tm-30) REVERT: E 12 PHE cc_start: 0.6481 (t80) cc_final: 0.6118 (m-10) REVERT: E 92 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6403 (t80) REVERT: E 140 GLU cc_start: 0.5901 (mt-10) cc_final: 0.5610 (mt-10) REVERT: E 141 PHE cc_start: 0.8107 (t80) cc_final: 0.7901 (t80) REVERT: D 213 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6663 (p90) REVERT: D 434 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7901 (mt) REVERT: D 476 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8175 (tm-30) REVERT: C 213 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6659 (p90) REVERT: C 434 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7928 (mt) REVERT: C 476 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8150 (tm-30) REVERT: B 213 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6623 (p90) REVERT: B 476 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8178 (tm-30) REVERT: H 12 PHE cc_start: 0.6438 (t80) cc_final: 0.6076 (m-10) REVERT: H 92 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6460 (t80) REVERT: G 12 PHE cc_start: 0.6448 (t80) cc_final: 0.6086 (m-10) REVERT: G 92 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6376 (t80) REVERT: F 12 PHE cc_start: 0.6429 (t80) cc_final: 0.5928 (m-10) REVERT: F 141 PHE cc_start: 0.8094 (t80) cc_final: 0.7811 (t80) outliers start: 124 outliers final: 96 residues processed: 489 average time/residue: 0.2849 time to fit residues: 236.9596 Evaluate side-chains 493 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 387 time to evaluate : 2.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 84 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 248 optimal weight: 10.0000 chunk 17 optimal weight: 40.0000 chunk 147 optimal weight: 0.3980 chunk 276 optimal weight: 4.9990 chunk 159 optimal weight: 0.0870 chunk 5 optimal weight: 6.9990 chunk 310 optimal weight: 50.0000 chunk 33 optimal weight: 0.6980 chunk 299 optimal weight: 50.0000 overall best weight: 2.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.222770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.190942 restraints weight = 36251.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.189616 restraints weight = 84819.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.185317 restraints weight = 38640.113| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 25188 Z= 0.181 Angle : 0.589 7.275 34444 Z= 0.308 Chirality : 0.042 0.140 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.071 52.827 3590 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 6.64 % Allowed : 29.46 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.15), residues: 3340 helix: 1.67 (0.13), residues: 1936 sheet: -0.35 (0.32), residues: 208 loop : -0.59 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 517 HIS 0.009 0.001 HIS B 364 PHE 0.014 0.001 PHE A 617 TYR 0.017 0.002 TYR B 423 ARG 0.003 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 1485) hydrogen bonds : angle 3.90241 ( 4332) covalent geometry : bond 0.00431 (25188) covalent geometry : angle 0.58919 (34444) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 381 time to evaluate : 2.764 Fit side-chains REVERT: A 213 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6782 (p90) REVERT: A 476 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8105 (tm-30) REVERT: E 12 PHE cc_start: 0.6515 (t80) cc_final: 0.6042 (m-10) REVERT: E 92 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6453 (t80) REVERT: E 140 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6030 (mt-10) REVERT: D 213 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6789 (p90) REVERT: D 476 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 213 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6776 (p90) REVERT: C 476 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8118 (tm-30) REVERT: B 213 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6710 (p90) REVERT: B 476 GLN cc_start: 0.8279 (tm-30) cc_final: 0.7881 (tm-30) REVERT: H 12 PHE cc_start: 0.6606 (t80) cc_final: 0.6034 (m-10) REVERT: H 92 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.6476 (t80) REVERT: H 129 ASP cc_start: 0.4016 (t0) cc_final: 0.3788 (t0) REVERT: H 140 GLU cc_start: 0.6189 (mt-10) cc_final: 0.5863 (mt-10) REVERT: G 12 PHE cc_start: 0.6587 (t80) cc_final: 0.6028 (m-10) REVERT: G 92 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6408 (t80) REVERT: F 12 PHE cc_start: 0.6475 (t80) cc_final: 0.5820 (m-10) REVERT: F 141 PHE cc_start: 0.8556 (t80) cc_final: 0.8243 (t80) outliers start: 152 outliers final: 115 residues processed: 505 average time/residue: 0.2702 time to fit residues: 232.1203 Evaluate side-chains 498 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 376 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 583 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 151 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 323 optimal weight: 40.0000 chunk 335 optimal weight: 10.0000 chunk 93 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 199 optimal weight: 0.5980 chunk 170 optimal weight: 0.0270 chunk 320 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 overall best weight: 1.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.225875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.192075 restraints weight = 36014.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.193935 restraints weight = 78111.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.194047 restraints weight = 41962.996| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25188 Z= 0.127 Angle : 0.554 7.589 34444 Z= 0.285 Chirality : 0.040 0.142 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.905 52.379 3590 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.59 % Allowed : 31.51 % Favored : 63.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.15), residues: 3340 helix: 1.81 (0.13), residues: 1932 sheet: -0.22 (0.32), residues: 208 loop : -0.54 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 295 HIS 0.005 0.001 HIS D 364 PHE 0.014 0.001 PHE D 429 TYR 0.014 0.001 TYR D 371 ARG 0.003 0.000 ARG E 126 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 1485) hydrogen bonds : angle 3.73739 ( 4332) covalent geometry : bond 0.00285 (25188) covalent geometry : angle 0.55443 (34444) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 409 time to evaluate : 2.933 Fit side-chains REVERT: A 213 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6580 (p90) REVERT: E 12 PHE cc_start: 0.6355 (t80) cc_final: 0.6049 (m-10) REVERT: E 92 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6429 (t80) REVERT: E 140 GLU cc_start: 0.6040 (mt-10) cc_final: 0.5701 (mt-10) REVERT: E 141 PHE cc_start: 0.8273 (t80) cc_final: 0.8056 (t80) REVERT: D 213 TYR cc_start: 0.7227 (OUTLIER) cc_final: 0.6579 (p90) REVERT: C 213 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6581 (p90) REVERT: B 213 TYR cc_start: 0.7246 (OUTLIER) cc_final: 0.6570 (p90) REVERT: H 12 PHE cc_start: 0.6443 (t80) cc_final: 0.6050 (m-10) REVERT: H 92 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6425 (t80) REVERT: G 12 PHE cc_start: 0.6366 (t80) cc_final: 0.6005 (m-10) REVERT: G 92 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6222 (t80) REVERT: F 12 PHE cc_start: 0.6363 (t80) cc_final: 0.5807 (m-10) outliers start: 105 outliers final: 79 residues processed: 484 average time/residue: 0.3074 time to fit residues: 250.9153 Evaluate side-chains 477 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 391 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 583 HIS Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 710 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 583 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 223 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 270 optimal weight: 2.9990 chunk 318 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 221 optimal weight: 7.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS B 46 ASN B 56 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.221820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.185072 restraints weight = 36112.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.183606 restraints weight = 75143.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.185458 restraints weight = 58564.509| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25188 Z= 0.172 Angle : 0.604 7.737 34444 Z= 0.312 Chirality : 0.042 0.146 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.006 53.079 3590 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 6.12 % Allowed : 31.12 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.15), residues: 3340 helix: 1.73 (0.13), residues: 1936 sheet: -0.10 (0.33), residues: 208 loop : -0.57 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 222 HIS 0.008 0.001 HIS B 364 PHE 0.026 0.001 PHE C 95 TYR 0.016 0.002 TYR B 423 ARG 0.004 0.000 ARG D 677 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 1485) hydrogen bonds : angle 3.83622 ( 4332) covalent geometry : bond 0.00408 (25188) covalent geometry : angle 0.60430 (34444) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 387 time to evaluate : 2.803 Fit side-chains REVERT: A 213 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6727 (p90) REVERT: A 305 PRO cc_start: 0.6293 (Cg_endo) cc_final: 0.5966 (Cg_exo) REVERT: A 476 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8186 (tm-30) REVERT: E 12 PHE cc_start: 0.6462 (t80) cc_final: 0.6032 (m-10) REVERT: E 92 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6490 (t80) REVERT: E 140 GLU cc_start: 0.6321 (mt-10) cc_final: 0.6013 (mt-10) REVERT: E 141 PHE cc_start: 0.8523 (t80) cc_final: 0.8138 (t80) REVERT: D 213 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.6746 (p90) REVERT: D 305 PRO cc_start: 0.6294 (Cg_endo) cc_final: 0.5956 (Cg_exo) REVERT: D 476 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8280 (tm-30) REVERT: C 213 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6746 (p90) REVERT: C 476 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 213 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6743 (p90) REVERT: B 476 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8332 (tm-30) REVERT: H 12 PHE cc_start: 0.6525 (t80) cc_final: 0.6022 (m-10) REVERT: H 92 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6460 (t80) REVERT: G 12 PHE cc_start: 0.6490 (t80) cc_final: 0.6011 (m-10) REVERT: G 92 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6238 (t80) REVERT: G 141 PHE cc_start: 0.8465 (t80) cc_final: 0.8257 (t80) REVERT: F 12 PHE cc_start: 0.6335 (t80) cc_final: 0.5752 (m-10) outliers start: 140 outliers final: 117 residues processed: 494 average time/residue: 0.2876 time to fit residues: 240.5410 Evaluate side-chains 507 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 383 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 669 ILE Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 430 THR Chi-restraints excluded: chain D residue 442 ILE Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 472 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 516 THR Chi-restraints excluded: chain C residue 583 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 442 ILE Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 463 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 ILE Chi-restraints excluded: chain B residue 583 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 669 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 62 optimal weight: 0.6980 chunk 252 optimal weight: 0.6980 chunk 328 optimal weight: 20.0000 chunk 180 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 194 optimal weight: 0.0020 chunk 258 optimal weight: 1.9990 chunk 190 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 56 HIS D 46 ASN D 56 HIS C 56 HIS B 56 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.226681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.191815 restraints weight = 36399.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.191400 restraints weight = 73964.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.193090 restraints weight = 56363.575| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25188 Z= 0.112 Angle : 0.560 10.342 34444 Z= 0.282 Chirality : 0.040 0.138 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.732 51.617 3590 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.72 % Allowed : 33.48 % Favored : 62.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.15), residues: 3340 helix: 1.95 (0.13), residues: 1932 sheet: 0.00 (0.33), residues: 208 loop : -0.44 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 222 HIS 0.004 0.001 HIS C 56 PHE 0.026 0.001 PHE F 141 TYR 0.011 0.001 TYR C 371 ARG 0.009 0.000 ARG F 126 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 1485) hydrogen bonds : angle 3.63354 ( 4332) covalent geometry : bond 0.00237 (25188) covalent geometry : angle 0.55984 (34444) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 397 time to evaluate : 2.997 Fit side-chains REVERT: A 213 TYR cc_start: 0.7208 (OUTLIER) cc_final: 0.6551 (p90) REVERT: E 12 PHE cc_start: 0.6414 (t80) cc_final: 0.6058 (m-10) REVERT: E 92 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6257 (t80) REVERT: E 139 GLU cc_start: 0.7934 (mp0) cc_final: 0.7681 (mp0) REVERT: E 140 GLU cc_start: 0.5914 (mt-10) cc_final: 0.5700 (mt-10) REVERT: E 141 PHE cc_start: 0.8256 (t80) cc_final: 0.8046 (t80) REVERT: D 213 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6481 (p90) REVERT: C 213 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6497 (p90) REVERT: B 213 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6480 (p90) REVERT: H 12 PHE cc_start: 0.6361 (t80) cc_final: 0.5988 (m-10) REVERT: H 92 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6324 (t80) REVERT: G 12 PHE cc_start: 0.6382 (t80) cc_final: 0.6002 (m-10) REVERT: G 92 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6108 (t80) REVERT: G 141 PHE cc_start: 0.8152 (t80) cc_final: 0.7892 (t80) REVERT: F 12 PHE cc_start: 0.6324 (t80) cc_final: 0.5785 (m-10) REVERT: F 135 GLN cc_start: 0.5715 (pp30) cc_final: 0.5203 (pm20) REVERT: F 141 PHE cc_start: 0.8245 (t80) cc_final: 0.8027 (t80) outliers start: 85 outliers final: 70 residues processed: 456 average time/residue: 0.3295 time to fit residues: 250.5361 Evaluate side-chains 463 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 386 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 472 THR Chi-restraints excluded: chain C residue 583 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 475 PHE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 583 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 117 THR Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 74 optimal weight: 9.9990 chunk 327 optimal weight: 0.0570 chunk 199 optimal weight: 2.9990 chunk 170 optimal weight: 0.1980 chunk 131 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 overall best weight: 1.6504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 46 ASN C 56 HIS B 56 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.223946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.189002 restraints weight = 36291.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.190873 restraints weight = 78233.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.191739 restraints weight = 44490.248| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25188 Z= 0.139 Angle : 0.586 10.169 34444 Z= 0.299 Chirality : 0.041 0.138 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.760 51.638 3590 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.72 % Allowed : 32.87 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.15), residues: 3340 helix: 1.93 (0.13), residues: 1932 sheet: 0.13 (0.33), residues: 208 loop : -0.45 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 517 HIS 0.006 0.001 HIS C 364 PHE 0.028 0.001 PHE A 95 TYR 0.012 0.001 TYR B 423 ARG 0.004 0.000 ARG D 677 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 1485) hydrogen bonds : angle 3.67210 ( 4332) covalent geometry : bond 0.00326 (25188) covalent geometry : angle 0.58583 (34444) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 389 time to evaluate : 2.727 Fit side-chains REVERT: A 476 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8191 (tm-30) REVERT: E 12 PHE cc_start: 0.6399 (t80) cc_final: 0.6051 (m-10) REVERT: E 92 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6374 (t80) REVERT: E 139 GLU cc_start: 0.7742 (mp0) cc_final: 0.7495 (mp0) REVERT: E 140 GLU cc_start: 0.5906 (mt-10) cc_final: 0.5668 (mt-10) REVERT: D 476 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 476 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 476 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8216 (tm-30) REVERT: H 12 PHE cc_start: 0.6362 (t80) cc_final: 0.5992 (m-10) REVERT: H 92 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6393 (t80) REVERT: H 141 PHE cc_start: 0.8216 (t80) cc_final: 0.7944 (t80) REVERT: G 12 PHE cc_start: 0.6379 (t80) cc_final: 0.5999 (m-10) REVERT: G 92 PHE cc_start: 0.7056 (OUTLIER) cc_final: 0.6250 (t80) REVERT: F 12 PHE cc_start: 0.6365 (t80) cc_final: 0.5836 (m-10) outliers start: 85 outliers final: 78 residues processed: 455 average time/residue: 0.2972 time to fit residues: 229.2201 Evaluate side-chains 464 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 383 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 418 SER Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 583 HIS Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 583 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 583 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 145 MET Chi-restraints excluded: chain F residue 68 PHE Chi-restraints excluded: chain F residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 18 optimal weight: 7.9990 chunk 269 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 256 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 120 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 311 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.226117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.193170 restraints weight = 36086.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.195122 restraints weight = 79924.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.194720 restraints weight = 40367.778| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25188 Z= 0.119 Angle : 0.590 10.115 34444 Z= 0.297 Chirality : 0.040 0.180 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.691 51.611 3590 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.54 % Allowed : 33.26 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.15), residues: 3340 helix: 1.96 (0.13), residues: 1932 sheet: 0.15 (0.33), residues: 208 loop : -0.37 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 295 HIS 0.004 0.001 HIS C 364 PHE 0.032 0.001 PHE A 95 TYR 0.011 0.001 TYR C 371 ARG 0.003 0.000 ARG D 333 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 1485) hydrogen bonds : angle 3.60862 ( 4332) covalent geometry : bond 0.00264 (25188) covalent geometry : angle 0.59044 (34444) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 399 time to evaluate : 2.756 Fit side-chains REVERT: E 12 PHE cc_start: 0.6436 (t80) cc_final: 0.6039 (m-10) REVERT: E 92 PHE cc_start: 0.7138 (OUTLIER) cc_final: 0.6376 (t80) REVERT: E 139 GLU cc_start: 0.7814 (mp0) cc_final: 0.7534 (mp0) REVERT: H 12 PHE cc_start: 0.6451 (t80) cc_final: 0.6024 (m-10) REVERT: H 92 PHE cc_start: 0.7166 (OUTLIER) cc_final: 0.6371 (t80) REVERT: G 12 PHE cc_start: 0.6475 (t80) cc_final: 0.6029 (m-10) REVERT: G 92 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6149 (t80) REVERT: F 12 PHE cc_start: 0.6388 (t80) cc_final: 0.5823 (m-10) REVERT: F 135 GLN cc_start: 0.5485 (pp30) cc_final: 0.5015 (pm20) REVERT: F 141 PHE cc_start: 0.8323 (t80) cc_final: 0.8093 (t80) outliers start: 81 outliers final: 72 residues processed: 460 average time/residue: 0.2914 time to fit residues: 227.0512 Evaluate side-chains 463 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 388 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 50 CYS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 583 HIS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 92 PHE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 50 CYS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 358 VAL Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 671 THR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 29 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 CYS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 583 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 29 ASN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 50 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 583 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 92 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain F residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 42 optimal weight: 0.5980 chunk 261 optimal weight: 0.4980 chunk 295 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 245 optimal weight: 0.7980 chunk 330 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 0.5980 chunk 166 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS D 56 HIS C 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.228484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.196869 restraints weight = 36247.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.194159 restraints weight = 75564.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.189515 restraints weight = 38348.056| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25188 Z= 0.118 Angle : 0.592 9.950 34444 Z= 0.297 Chirality : 0.040 0.194 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.632 51.273 3590 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.45 % Allowed : 33.17 % Favored : 63.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.15), residues: 3340 helix: 1.99 (0.13), residues: 1932 sheet: 0.25 (0.33), residues: 208 loop : -0.34 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 517 HIS 0.004 0.001 HIS D 364 PHE 0.014 0.001 PHE H 141 TYR 0.010 0.001 TYR C 371 ARG 0.003 0.000 ARG G 126 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 1485) hydrogen bonds : angle 3.60247 ( 4332) covalent geometry : bond 0.00259 (25188) covalent geometry : angle 0.59150 (34444) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7031.31 seconds wall clock time: 123 minutes 58.34 seconds (7438.34 seconds total)