Starting phenix.real_space_refine on Mon Aug 25 01:45:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eow_28487/08_2025/8eow_28487.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eow_28487/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8eow_28487/08_2025/8eow_28487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eow_28487/08_2025/8eow_28487.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eow_28487/08_2025/8eow_28487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eow_28487/08_2025/8eow_28487.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 14, 'ARG:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 11, 'GLN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU%COO:plan': 1} 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: {'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 4} 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: {'GLU:plan': 14, 'ARG:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 11, 'GLN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU%COO:plan': 1} 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: {'GLU:plan': 14, 'ARG:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 11, 'GLN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU%COO:plan': 1} 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: {'GLU:plan': 14, 'ARG:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 11, 'GLN:plan1': 11, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU%COO:plan': 1} 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: {'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 4} 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: {'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 4} 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: {'GLU:plan': 15, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASP:plan': 9, 'ARG:plan': 5, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 142 Time building chain proxies: 6.88, per 1000 atoms: 0.28 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: 2.66 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.7 microseconds 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: 0.99 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: 5.47 Time building geometry restraints manager: 3.38 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: 0.05 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.410 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- 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 : 8.13 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG D 677 TYR 0.016 0.001 TYR C 371 PHE 0.010 0.001 PHE A 429 TRP 0.011 0.001 TRP D 295 HIS 0.006 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00272 (25188) covalent geometry : angle 0.57272 (34444) hydrogen bonds : bond 0.11266 ( 1485) hydrogen bonds : angle 4.64289 ( 4332) *********************** 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 : 0.909 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: 0.1412 time to fit residues: 98.3984 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 : 0.991 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 20.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 247 ASN A 290 ASN A 583 HIS D 56 HIS D 247 ASN D 290 ASN D 583 HIS C 56 HIS C 247 ASN C 290 ASN C 583 HIS B 56 HIS B 247 ASN B 290 ASN B 583 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.221771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.184788 restraints weight = 36733.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.181144 restraints weight = 69587.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183728 restraints weight = 58183.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.184043 restraints weight = 31033.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.188099 restraints weight = 25788.728| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25188 Z= 0.188 Angle : 0.580 7.131 34444 Z= 0.308 Chirality : 0.042 0.145 4052 Planarity : 0.004 0.054 4420 Dihedral : 4.325 52.472 3604 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.76 % Allowed : 28.93 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.15), residues: 3340 helix: 1.76 (0.13), residues: 1936 sheet: -0.85 (0.34), residues: 208 loop : -0.48 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 677 TYR 0.017 0.002 TYR B 423 PHE 0.014 0.001 PHE B 617 TRP 0.010 0.002 TRP C 517 HIS 0.010 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00444 (25188) covalent geometry : angle 0.58035 (34444) hydrogen bonds : bond 0.04878 ( 1485) hydrogen bonds : angle 4.00834 ( 4332) *********************** 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 497 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 388 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8263 (tm-30) REVERT: E 12 PHE cc_start: 0.6619 (t80) cc_final: 0.6080 (m-10) REVERT: E 141 PHE cc_start: 0.8136 (t80) cc_final: 0.7796 (t80) REVERT: D 476 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8295 (tm-30) REVERT: C 476 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 292 LEU cc_start: 0.8196 (tt) cc_final: 0.7472 (mt) REVERT: B 476 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8271 (tm-30) REVERT: H 12 PHE cc_start: 0.6612 (t80) cc_final: 0.6078 (m-10) REVERT: H 92 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6514 (t80) REVERT: G 12 PHE cc_start: 0.6608 (t80) cc_final: 0.6100 (m-10) REVERT: G 92 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6422 (t80) REVERT: F 12 PHE cc_start: 0.6504 (t80) cc_final: 0.5906 (m-10) REVERT: F 92 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6767 (t80) outliers start: 109 outliers final: 62 residues processed: 468 average time/residue: 0.1368 time to fit residues: 109.9697 Evaluate side-chains 445 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 380 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 223 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL 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 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 223 ILE 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 378 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 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 223 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 263 VAL 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 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 378 ILE Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 463 LEU 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 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 322 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 260 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 81 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 93 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4615 r_free = 0.4615 target = 0.226444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.189644 restraints weight = 36760.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182018 restraints weight = 31751.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.182685 restraints weight = 35976.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.183582 restraints weight = 29336.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.185102 restraints weight = 21233.900| |-----------------------------------------------------------------------------| r_work (final): 0.4077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25188 Z= 0.107 Angle : 0.508 7.285 34444 Z= 0.264 Chirality : 0.039 0.140 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.849 51.069 3592 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.98 % Allowed : 29.72 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.15), residues: 3340 helix: 1.94 (0.13), residues: 1936 sheet: -0.54 (0.32), residues: 208 loop : -0.38 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 677 TYR 0.015 0.001 TYR C 371 PHE 0.013 0.001 PHE B 429 TRP 0.011 0.001 TRP C 222 HIS 0.003 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00220 (25188) covalent geometry : angle 0.50759 (34444) hydrogen bonds : bond 0.03983 ( 1485) hydrogen bonds : angle 3.69751 ( 4332) *********************** 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 506 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 415 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: E 12 PHE cc_start: 0.6660 (t80) cc_final: 0.5962 (m-10) REVERT: E 92 PHE cc_start: 0.7000 (OUTLIER) cc_final: 0.6245 (t80) REVERT: E 140 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6184 (mt-10) REVERT: E 141 PHE cc_start: 0.8655 (t80) cc_final: 0.8442 (t80) REVERT: H 12 PHE cc_start: 0.6689 (t80) cc_final: 0.6002 (m-10) REVERT: H 92 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6345 (t80) REVERT: G 12 PHE cc_start: 0.6681 (t80) cc_final: 0.5994 (m-10) REVERT: G 92 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6399 (t80) REVERT: F 12 PHE cc_start: 0.6432 (t80) cc_final: 0.5747 (m-10) REVERT: F 92 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6519 (t80) REVERT: F 141 PHE cc_start: 0.8566 (t80) cc_final: 0.8343 (t80) outliers start: 91 outliers final: 52 residues processed: 480 average time/residue: 0.1392 time to fit residues: 114.2994 Evaluate side-chains 445 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 389 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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 136 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 392 LEU 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 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 233 ILE Chi-restraints excluded: chain D residue 234 LEU 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 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 233 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 583 HIS 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 136 PHE Chi-restraints excluded: chain B residue 205 THR 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 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 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 Chi-restraints excluded: chain F residue 130 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 185 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 212 optimal weight: 0.2980 chunk 10 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 173 optimal weight: 7.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.223136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.191696 restraints weight = 36217.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.190425 restraints weight = 82668.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.186838 restraints weight = 36294.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.186121 restraints weight = 37195.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.186288 restraints weight = 30332.803| |-----------------------------------------------------------------------------| r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 25188 Z= 0.193 Angle : 0.589 7.329 34444 Z= 0.310 Chirality : 0.042 0.176 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.060 51.938 3592 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.33 % Allowed : 29.55 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.15), residues: 3340 helix: 1.74 (0.13), residues: 1936 sheet: -0.40 (0.32), residues: 208 loop : -0.51 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 336 TYR 0.018 0.002 TYR D 423 PHE 0.020 0.002 PHE B 95 TRP 0.010 0.002 TRP D 517 HIS 0.011 0.002 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00462 (25188) covalent geometry : angle 0.58915 (34444) hydrogen bonds : bond 0.04864 ( 1485) hydrogen bonds : angle 3.91642 ( 4332) *********************** 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 504 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 382 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 476 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8220 (tm-30) REVERT: E 12 PHE cc_start: 0.6594 (t80) cc_final: 0.6084 (m-10) REVERT: E 92 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6462 (t80) REVERT: E 140 GLU cc_start: 0.6172 (mt-10) cc_final: 0.5790 (mt-10) REVERT: E 141 PHE cc_start: 0.8393 (t80) cc_final: 0.8139 (t80) REVERT: D 476 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 476 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8301 (tm-30) REVERT: B 476 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8297 (tm-30) REVERT: H 12 PHE cc_start: 0.6635 (t80) cc_final: 0.6084 (m-10) REVERT: H 92 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6498 (t80) REVERT: G 12 PHE cc_start: 0.6638 (t80) cc_final: 0.6085 (m-10) REVERT: G 92 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6432 (t80) REVERT: G 141 PHE cc_start: 0.8299 (t80) cc_final: 0.8084 (t80) REVERT: F 12 PHE cc_start: 0.6511 (t80) cc_final: 0.5873 (m-10) REVERT: F 133 ASP cc_start: 0.5238 (p0) cc_final: 0.4988 (p0) outliers start: 122 outliers final: 95 residues processed: 475 average time/residue: 0.1286 time to fit residues: 104.7434 Evaluate side-chains 477 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 379 time to evaluate : 0.891 ------------------------------------------------------------------------------- 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 131 SER Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 378 ILE Chi-restraints excluded: chain A residue 463 LEU 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 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 116 LEU Chi-restraints excluded: chain E residue 145 MET 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 131 SER Chi-restraints excluded: chain D residue 223 ILE Chi-restraints excluded: chain D residue 233 ILE 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 341 LEU 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 473 THR Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 583 HIS Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 645 ILE 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 131 SER Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 233 ILE 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 378 ILE 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 473 THR Chi-restraints excluded: chain C residue 474 ILE 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 645 ILE Chi-restraints excluded: chain C residue 710 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 131 SER Chi-restraints excluded: chain B residue 205 THR 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 297 VAL 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 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 474 ILE 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 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 Chi-restraints excluded: chain F residue 130 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 237 optimal weight: 0.1980 chunk 134 optimal weight: 9.9990 chunk 69 optimal weight: 40.0000 chunk 27 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 50.0000 chunk 152 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 291 optimal weight: 8.9990 chunk 46 optimal weight: 0.5980 chunk 92 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 = 0.4588 r_free = 0.4588 target = 0.223887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.189093 restraints weight = 36460.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.189670 restraints weight = 78163.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.190956 restraints weight = 54715.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.191372 restraints weight = 32448.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.191930 restraints weight = 27851.561| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25188 Z= 0.142 Angle : 0.547 7.385 34444 Z= 0.286 Chirality : 0.041 0.139 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.002 52.044 3592 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 6.16 % Allowed : 28.72 % Favored : 65.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.15), residues: 3340 helix: 1.78 (0.13), residues: 1936 sheet: -0.29 (0.32), residues: 208 loop : -0.47 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 126 TYR 0.014 0.001 TYR C 371 PHE 0.013 0.001 PHE B 429 TRP 0.009 0.001 TRP A 222 HIS 0.006 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00331 (25188) covalent geometry : angle 0.54673 (34444) hydrogen bonds : bond 0.04442 ( 1485) hydrogen bonds : angle 3.76551 ( 4332) *********************** 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 536 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 395 time to evaluate : 0.712 Fit side-chains REVERT: A 213 TYR cc_start: 0.7235 (OUTLIER) cc_final: 0.6659 (p90) REVERT: A 432 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.7959 (m) REVERT: A 476 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8226 (tm-30) REVERT: E 12 PHE cc_start: 0.6483 (t80) cc_final: 0.6113 (m-10) REVERT: E 92 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6372 (t80) REVERT: E 140 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5721 (mt-10) REVERT: E 141 PHE cc_start: 0.8056 (t80) cc_final: 0.7853 (t80) REVERT: D 213 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6667 (p90) REVERT: D 432 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.7957 (m) REVERT: D 476 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8218 (tm-30) REVERT: C 213 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6653 (p90) REVERT: C 432 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.7963 (m) REVERT: C 434 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7930 (mt) REVERT: C 476 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 213 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6568 (p90) REVERT: B 432 THR cc_start: 0.8885 (OUTLIER) cc_final: 0.7953 (m) REVERT: B 434 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7914 (mt) REVERT: B 476 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8219 (tm-30) REVERT: H 12 PHE cc_start: 0.6517 (t80) cc_final: 0.6060 (m-10) REVERT: H 92 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6416 (t80) REVERT: H 140 GLU cc_start: 0.5692 (mt-10) cc_final: 0.5466 (mt-10) REVERT: G 12 PHE cc_start: 0.6526 (t80) cc_final: 0.6076 (m-10) REVERT: G 92 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6409 (t80) REVERT: F 12 PHE cc_start: 0.6481 (t80) cc_final: 0.5897 (m-10) REVERT: F 141 PHE cc_start: 0.8128 (t80) cc_final: 0.7857 (t80) outliers start: 141 outliers final: 97 residues processed: 502 average time/residue: 0.1337 time to fit residues: 114.6278 Evaluate side-chains 501 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 391 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 260 ILE 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 432 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 513 ILE 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 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 E residue 145 MET 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 234 LEU Chi-restraints excluded: chain D residue 341 LEU 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 432 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 513 ILE Chi-restraints excluded: chain D residue 583 HIS 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 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 131 SER Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 223 ILE Chi-restraints excluded: chain C residue 233 ILE 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 418 SER Chi-restraints excluded: chain C residue 432 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 513 ILE Chi-restraints excluded: chain C residue 583 HIS Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 669 ILE 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 131 SER 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 430 THR Chi-restraints excluded: chain B residue 432 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 513 ILE 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 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 117 THR Chi-restraints excluded: chain F residue 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 130 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 24 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 326 optimal weight: 20.0000 chunk 214 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.224696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.191963 restraints weight = 36456.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.193908 restraints weight = 79496.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.192856 restraints weight = 36850.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.192159 restraints weight = 33143.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.192466 restraints weight = 27233.437| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 25188 Z= 0.161 Angle : 0.575 7.462 34444 Z= 0.300 Chirality : 0.041 0.140 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.040 51.073 3592 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 6.82 % Allowed : 28.15 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.15), residues: 3340 helix: 1.74 (0.13), residues: 1936 sheet: -0.15 (0.32), residues: 208 loop : -0.51 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.016 0.001 TYR C 423 PHE 0.022 0.001 PHE B 95 TRP 0.009 0.001 TRP C 295 HIS 0.008 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00380 (25188) covalent geometry : angle 0.57486 (34444) hydrogen bonds : bond 0.04630 ( 1485) hydrogen bonds : angle 3.81490 ( 4332) *********************** 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 555 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 399 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6627 (p90) REVERT: A 432 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 476 GLN cc_start: 0.8588 (tm-30) cc_final: 0.8179 (tm-30) REVERT: E 12 PHE cc_start: 0.6418 (t80) cc_final: 0.6079 (m-10) REVERT: E 92 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6430 (t80) REVERT: E 139 GLU cc_start: 0.7784 (mp0) cc_final: 0.7518 (mp0) REVERT: E 140 GLU cc_start: 0.6036 (mt-10) cc_final: 0.5619 (mt-10) REVERT: E 141 PHE cc_start: 0.8251 (t80) cc_final: 0.7994 (t80) REVERT: D 213 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6714 (p90) REVERT: D 476 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 213 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6705 (p90) REVERT: C 476 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 213 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6598 (p90) REVERT: B 476 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8174 (tm-30) REVERT: H 12 PHE cc_start: 0.6448 (t80) cc_final: 0.6040 (m-10) REVERT: H 92 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6457 (t80) REVERT: G 12 PHE cc_start: 0.6483 (t80) cc_final: 0.6042 (m-10) REVERT: G 92 PHE cc_start: 0.7106 (OUTLIER) cc_final: 0.6290 (t80) REVERT: G 141 PHE cc_start: 0.8104 (t80) cc_final: 0.7892 (t80) REVERT: F 12 PHE cc_start: 0.6308 (t80) cc_final: 0.5809 (m-10) outliers start: 156 outliers final: 119 residues processed: 517 average time/residue: 0.1233 time to fit residues: 109.4453 Evaluate side-chains 517 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 390 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 131 SER 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 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 432 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 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 E residue 145 MET 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 131 SER 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 341 LEU 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 432 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 583 HIS Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 645 ILE Chi-restraints excluded: chain D residue 671 THR 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 131 SER 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 432 THR 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 645 ILE Chi-restraints excluded: chain C residue 710 VAL 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 131 SER 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 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 432 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 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 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 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 290 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 30 optimal weight: 40.0000 chunk 34 optimal weight: 3.9990 chunk 254 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 260 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.220987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.187223 restraints weight = 36007.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.188996 restraints weight = 81054.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.188068 restraints weight = 37655.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.187536 restraints weight = 30395.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.188061 restraints weight = 22334.002| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 25188 Z= 0.198 Angle : 0.631 8.119 34444 Z= 0.327 Chirality : 0.043 0.140 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.203 51.245 3592 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 7.08 % Allowed : 28.45 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.15), residues: 3340 helix: 1.61 (0.13), residues: 1936 sheet: -0.23 (0.37), residues: 176 loop : -0.57 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 126 TYR 0.019 0.002 TYR C 423 PHE 0.014 0.002 PHE B 429 TRP 0.015 0.002 TRP B 222 HIS 0.010 0.002 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00477 (25188) covalent geometry : angle 0.63092 (34444) hydrogen bonds : bond 0.05033 ( 1485) hydrogen bonds : angle 3.94562 ( 4332) *********************** 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 551 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 389 time to evaluate : 0.999 Fit side-chains REVERT: A 213 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6807 (p90) REVERT: A 305 PRO cc_start: 0.6262 (Cg_endo) cc_final: 0.5935 (Cg_exo) REVERT: A 476 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8193 (tm-30) REVERT: E 12 PHE cc_start: 0.6418 (t80) cc_final: 0.6047 (m-10) REVERT: E 92 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6489 (t80) REVERT: E 139 GLU cc_start: 0.7779 (mp0) cc_final: 0.7546 (mp0) REVERT: E 140 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5841 (mt-10) REVERT: D 213 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6812 (p90) REVERT: D 476 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 213 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6811 (p90) REVERT: C 476 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 213 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.6815 (p90) REVERT: B 476 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8221 (tm-30) REVERT: H 12 PHE cc_start: 0.6507 (t80) cc_final: 0.6039 (m-10) REVERT: H 92 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6438 (t80) REVERT: H 129 ASP cc_start: 0.4093 (t0) cc_final: 0.3630 (t0) REVERT: H 140 GLU cc_start: 0.5977 (mt-10) cc_final: 0.5690 (mt-10) REVERT: G 12 PHE cc_start: 0.6483 (t80) cc_final: 0.6056 (m-10) REVERT: G 92 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.6217 (t80) REVERT: F 12 PHE cc_start: 0.6299 (t80) cc_final: 0.5738 (m-10) REVERT: F 141 PHE cc_start: 0.8309 (t80) cc_final: 0.8083 (t80) outliers start: 162 outliers final: 126 residues processed: 516 average time/residue: 0.1322 time to fit residues: 116.9905 Evaluate side-chains 516 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 383 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 131 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 231 THR 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 418 SER Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 432 THR 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 472 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 ILE 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 117 THR Chi-restraints excluded: chain E residue 145 MET 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 131 SER Chi-restraints excluded: chain D residue 213 TYR 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 341 LEU 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 432 THR 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 474 ILE 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 645 ILE Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain D residue 671 THR 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 131 SER Chi-restraints excluded: chain C residue 213 TYR 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 432 THR 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 474 ILE 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 645 ILE Chi-restraints excluded: chain C residue 669 ILE Chi-restraints excluded: chain C residue 671 THR 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 131 SER Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR 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 297 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 432 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 474 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 272 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 303 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 46 ASN C 56 HIS B 56 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.225115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.191472 restraints weight = 36234.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.193754 restraints weight = 79398.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.193413 restraints weight = 38090.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.192906 restraints weight = 27955.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.193420 restraints weight = 22543.132| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25188 Z= 0.134 Angle : 0.581 9.204 34444 Z= 0.296 Chirality : 0.041 0.143 4052 Planarity : 0.003 0.054 4420 Dihedral : 4.038 51.577 3592 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.81 % Allowed : 31.16 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.15), residues: 3340 helix: 1.79 (0.13), residues: 1936 sheet: -0.05 (0.33), residues: 208 loop : -0.55 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 677 TYR 0.013 0.001 TYR A 423 PHE 0.020 0.001 PHE H 141 TRP 0.013 0.001 TRP C 222 HIS 0.006 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00306 (25188) covalent geometry : angle 0.58069 (34444) hydrogen bonds : bond 0.04446 ( 1485) hydrogen bonds : angle 3.76967 ( 4332) *********************** 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 509 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 399 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6721 (p90) REVERT: A 305 PRO cc_start: 0.6204 (Cg_endo) cc_final: 0.5887 (Cg_exo) REVERT: E 12 PHE cc_start: 0.6422 (t80) cc_final: 0.6028 (m-10) REVERT: E 92 PHE cc_start: 0.7195 (OUTLIER) cc_final: 0.6432 (t80) REVERT: E 139 GLU cc_start: 0.7787 (mp0) cc_final: 0.7552 (mp0) REVERT: E 140 GLU cc_start: 0.6052 (mt-10) cc_final: 0.5848 (mt-10) REVERT: D 213 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6747 (p90) REVERT: D 305 PRO cc_start: 0.6185 (Cg_endo) cc_final: 0.5857 (Cg_exo) REVERT: C 213 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.6719 (p90) REVERT: B 213 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6724 (p90) REVERT: H 12 PHE cc_start: 0.6502 (t80) cc_final: 0.6023 (m-10) REVERT: H 92 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6410 (t80) REVERT: G 12 PHE cc_start: 0.6454 (t80) cc_final: 0.6005 (m-10) REVERT: G 92 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6173 (t80) REVERT: F 12 PHE cc_start: 0.6345 (t80) cc_final: 0.5770 (m-10) REVERT: F 141 PHE cc_start: 0.8272 (t80) cc_final: 0.8028 (t80) outliers start: 110 outliers final: 90 residues processed: 481 average time/residue: 0.1144 time to fit residues: 94.3632 Evaluate side-chains 484 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 387 time to evaluate : 0.775 ------------------------------------------------------------------------------- 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 513 ILE Chi-restraints excluded: chain A residue 570 PHE 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 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 341 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 473 THR Chi-restraints excluded: chain D residue 513 ILE Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 645 ILE 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 131 SER 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 430 THR Chi-restraints excluded: chain C residue 432 THR 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 473 THR Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 671 THR 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 131 SER 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 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 472 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 513 ILE 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 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 323 optimal weight: 40.0000 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 314 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 235 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.225382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.190838 restraints weight = 36312.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.191482 restraints weight = 78526.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.192920 restraints weight = 52489.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.192861 restraints weight = 33863.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.193969 restraints weight = 28138.063| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25188 Z= 0.118 Angle : 0.579 10.525 34444 Z= 0.291 Chirality : 0.040 0.142 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.875 53.619 3592 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.89 % Allowed : 31.99 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.15), residues: 3340 helix: 1.94 (0.13), residues: 1932 sheet: 0.05 (0.33), residues: 208 loop : -0.46 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 677 TYR 0.011 0.001 TYR A 371 PHE 0.028 0.001 PHE B 95 TRP 0.009 0.001 TRP C 295 HIS 0.004 0.001 HIS C 364 Details of bonding type rmsd covalent geometry : bond 0.00262 (25188) covalent geometry : angle 0.57882 (34444) hydrogen bonds : bond 0.04066 ( 1485) hydrogen bonds : angle 3.65674 ( 4332) *********************** 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 483 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 394 time to evaluate : 0.839 Fit side-chains REVERT: A 213 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.6631 (p90) REVERT: A 305 PRO cc_start: 0.6273 (Cg_endo) cc_final: 0.5953 (Cg_exo) REVERT: E 12 PHE cc_start: 0.6430 (t80) cc_final: 0.6056 (m-10) REVERT: E 92 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6309 (t80) REVERT: E 139 GLU cc_start: 0.7587 (mp0) cc_final: 0.7380 (mp0) REVERT: E 141 PHE cc_start: 0.8341 (t80) cc_final: 0.7969 (t80) REVERT: D 213 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.6627 (p90) REVERT: C 213 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6629 (p90) REVERT: B 213 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6610 (p90) REVERT: H 12 PHE cc_start: 0.6386 (t80) cc_final: 0.5987 (m-10) REVERT: H 92 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6269 (t80) REVERT: G 12 PHE cc_start: 0.6475 (t80) cc_final: 0.6038 (m-10) REVERT: G 92 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6026 (t80) REVERT: F 12 PHE cc_start: 0.6300 (t80) cc_final: 0.5767 (m-10) REVERT: F 92 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6494 (t80) outliers start: 89 outliers final: 76 residues processed: 457 average time/residue: 0.1327 time to fit residues: 102.9193 Evaluate side-chains 462 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 378 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 473 THR Chi-restraints excluded: chain A residue 570 PHE 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 105 LEU Chi-restraints excluded: chain E residue 117 THR 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 131 SER Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 341 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 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 669 ILE 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 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 669 ILE 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 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 143 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 137 optimal weight: 2.9990 chunk 254 optimal weight: 30.0000 chunk 228 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 chunk 246 optimal weight: 0.8980 chunk 237 optimal weight: 0.0970 chunk 194 optimal weight: 0.9980 chunk 328 optimal weight: 30.0000 chunk 220 optimal weight: 7.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- 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 = 0.4600 r_free = 0.4600 target = 0.226705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.192442 restraints weight = 36134.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.194488 restraints weight = 79041.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.194750 restraints weight = 41409.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.194680 restraints weight = 28059.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.195121 restraints weight = 23109.155| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25188 Z= 0.126 Angle : 0.597 10.925 34444 Z= 0.301 Chirality : 0.041 0.192 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.847 54.639 3592 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.85 % Allowed : 32.17 % Favored : 63.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.15), residues: 3340 helix: 1.96 (0.13), residues: 1932 sheet: 0.18 (0.34), residues: 208 loop : -0.41 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 677 TYR 0.011 0.001 TYR D 371 PHE 0.026 0.001 PHE H 141 TRP 0.010 0.001 TRP C 517 HIS 0.005 0.001 HIS A 364 Details of bonding type rmsd covalent geometry : bond 0.00287 (25188) covalent geometry : angle 0.59726 (34444) hydrogen bonds : bond 0.04102 ( 1485) hydrogen bonds : angle 3.65081 ( 4332) ********************** 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 479 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 391 time to evaluate : 0.904 Fit side-chains REVERT: A 213 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6677 (p90) REVERT: E 12 PHE cc_start: 0.6462 (t80) cc_final: 0.6041 (m-10) REVERT: E 92 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6342 (t80) REVERT: D 213 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6680 (p90) REVERT: C 213 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6693 (p90) REVERT: B 213 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6654 (p90) REVERT: H 12 PHE cc_start: 0.6422 (t80) cc_final: 0.5976 (m-10) REVERT: H 92 PHE cc_start: 0.7063 (OUTLIER) cc_final: 0.6387 (t80) REVERT: G 12 PHE cc_start: 0.6502 (t80) cc_final: 0.6018 (m-10) REVERT: G 92 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6121 (t80) REVERT: F 12 PHE cc_start: 0.6307 (t80) cc_final: 0.5746 (m-10) REVERT: F 92 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6621 (t80) outliers start: 88 outliers final: 79 residues processed: 453 average time/residue: 0.1358 time to fit residues: 105.1388 Evaluate side-chains 468 residues out of total 2996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 381 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 473 THR Chi-restraints excluded: chain A residue 570 PHE 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 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 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 131 SER Chi-restraints excluded: chain D residue 213 TYR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 341 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 448 ILE Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 595 VAL Chi-restraints excluded: chain D residue 669 ILE Chi-restraints excluded: chain D residue 671 THR 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 131 SER 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 669 ILE Chi-restraints excluded: chain C residue 671 THR 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 116 ILE Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 213 TYR 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 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 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 92 PHE Chi-restraints excluded: chain F residue 117 THR Chi-restraints excluded: chain F residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 219 optimal weight: 0.4980 chunk 157 optimal weight: 5.9990 chunk 265 optimal weight: 0.8980 chunk 259 optimal weight: 1.9990 chunk 221 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 333 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 330 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.4582 r_free = 0.4582 target = 0.224650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.192041 restraints weight = 36030.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.191718 restraints weight = 82800.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.188333 restraints weight = 36194.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.187716 restraints weight = 34652.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.187772 restraints weight = 29413.463| |-----------------------------------------------------------------------------| r_work (final): 0.4204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1744 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= 0.158 Angle : 0.639 12.060 34444 Z= 0.323 Chirality : 0.042 0.207 4052 Planarity : 0.003 0.055 4420 Dihedral : 3.961 54.479 3592 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.24 % Allowed : 32.21 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.15), residues: 3340 helix: 1.86 (0.13), residues: 1932 sheet: 0.20 (0.34), residues: 208 loop : -0.44 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 677 TYR 0.015 0.001 TYR A 423 PHE 0.026 0.001 PHE E 141 TRP 0.010 0.001 TRP D 517 HIS 0.007 0.001 HIS B 364 Details of bonding type rmsd covalent geometry : bond 0.00375 (25188) covalent geometry : angle 0.63856 (34444) hydrogen bonds : bond 0.04493 ( 1485) hydrogen bonds : angle 3.74492 ( 4332) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.60 seconds wall clock time: 64 minutes 22.66 seconds (3862.66 seconds total)