Starting phenix.real_space_refine on Sat Jul 4 12:10:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o6g_70173/07_2026/9o6g_70173.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o6g_70173/07_2026/9o6g_70173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9o6g_70173/07_2026/9o6g_70173.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o6g_70173/07_2026/9o6g_70173.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9o6g_70173/07_2026/9o6g_70173.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o6g_70173/07_2026/9o6g_70173.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 140 5.16 5 C 13226 2.51 5 N 3308 2.21 5 O 3573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20263 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4877 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 24, 'TRANS': 584} Chain: "B" Number of atoms: 4877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4877 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 24, 'TRANS': 584} Chain: "C" Number of atoms: 4877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4877 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 24, 'TRANS': 584} Chain: "D" Number of atoms: 4877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4877 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 24, 'TRANS': 584} Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {'CPL': 4, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3, 'CPL:plan-4': 4} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 197 Unusual residues: {'CPL': 4, 'ERG': 2, 'IT9': 1, 'PIO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3, 'CPL:plan-4': 4} Unresolved non-hydrogen planarities: 51 Chain: "C" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 141 Unusual residues: {'CPL': 3, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3, 'CPL:plan-4': 3} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {'CPL': 5, 'ERG': 2, 'PIO': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'CPL:plan-4': 5, 'CPL:plan-1': 3, 'CPL:plan-2': 3, 'CPL:plan-3': 3} Unresolved non-hydrogen planarities: 54 Time building chain proxies: 5.18, per 1000 atoms: 0.26 Number of scatterers: 20263 At special positions: 0 Unit cell: (137.78, 141.1, 122.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 16 15.00 O 3573 8.00 N 3308 7.00 C 13226 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 984.9 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4600 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 8 sheets defined 66.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 3.523A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.669A pdb=" N ASN A 56 " --> pdb=" O ALA A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.667A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.697A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.866A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.710A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.626A pdb=" N ILE A 202 " --> pdb=" O THR A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.712A pdb=" N VAL A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.601A pdb=" N GLN A 261 " --> pdb=" O GLN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 301 through 307 removed outlier: 3.641A pdb=" N ALA A 304 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.664A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 411 Proline residue: A 405 - end of helix removed outlier: 3.752A pdb=" N PHE A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 3.630A pdb=" N PHE A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 removed outlier: 3.615A pdb=" N THR A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 464 Processing helix chain 'A' and resid 465 through 470 removed outlier: 3.511A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 487 removed outlier: 4.503A pdb=" N THR A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 4.914A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.565A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 567 removed outlier: 3.704A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 587 removed outlier: 3.972A pdb=" N GLN A 587 " --> pdb=" O TRP A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 608 Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.708A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 removed outlier: 3.778A pdb=" N GLN B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 67 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.549A pdb=" N TYR B 89 " --> pdb=" O VAL B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 101 removed outlier: 3.597A pdb=" N ALA B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.706A pdb=" N LEU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.742A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.634A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.956A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 208 through 222 removed outlier: 4.382A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.527A pdb=" N GLN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.680A pdb=" N ALA B 304 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 411 Proline residue: B 405 - end of helix removed outlier: 3.756A pdb=" N PHE B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.620A pdb=" N PHE B 416 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 removed outlier: 3.518A pdb=" N THR B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.512A pdb=" N LEU B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.584A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 4.012A pdb=" N ILE B 480 " --> pdb=" O GLY B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 4.571A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.724A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.858A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 587 removed outlier: 3.651A pdb=" N GLN B 587 " --> pdb=" O TRP B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 608 removed outlier: 3.708A pdb=" N MET B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 removed outlier: 3.552A pdb=" N SER C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.687A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.558A pdb=" N GLU C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.795A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 140 removed outlier: 3.516A pdb=" N VAL C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 4.291A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.503A pdb=" N HIS C 185 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 212 through 222 removed outlier: 3.562A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 261 removed outlier: 3.576A pdb=" N GLN C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.885A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 3.720A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 411 Proline residue: C 405 - end of helix removed outlier: 3.692A pdb=" N PHE C 408 " --> pdb=" O ILE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.969A pdb=" N PHE C 416 " --> pdb=" O ALA C 412 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.593A pdb=" N LEU C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.545A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 472 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 487 Processing helix chain 'C' and resid 488 through 493 Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.720A pdb=" N MET C 497 " --> pdb=" O PHE C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.944A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.665A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 587 Processing helix chain 'C' and resid 588 through 608 removed outlier: 3.629A pdb=" N MET C 608 " --> pdb=" O LEU C 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.895A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 69 removed outlier: 3.674A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.773A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.892A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 3.880A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.855A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 140 removed outlier: 3.649A pdb=" N VAL D 133 " --> pdb=" O ASN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.621A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 186 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 222 removed outlier: 5.087A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.565A pdb=" N VAL D 235 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 removed outlier: 3.518A pdb=" N GLY D 251 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 303 through 308 Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.977A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 411 Proline residue: D 405 - end of helix removed outlier: 3.790A pdb=" N PHE D 408 " --> pdb=" O ILE D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.963A pdb=" N PHE D 416 " --> pdb=" O ALA D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 462 removed outlier: 3.576A pdb=" N LEU D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.697A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE D 472 " --> pdb=" O ALA D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 487 removed outlier: 4.678A pdb=" N THR D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE D 480 " --> pdb=" O GLY D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 4.898A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.578A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 567 Processing helix chain 'D' and resid 569 through 588 removed outlier: 3.741A pdb=" N GLN D 587 " --> pdb=" O TRP D 583 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU D 588 " --> pdb=" O ARG D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 608 removed outlier: 3.892A pdb=" N MET D 608 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.593A pdb=" N LEU D 612 " --> pdb=" O PRO D 609 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 265 through 270 removed outlier: 7.064A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 270 removed outlier: 5.643A pdb=" N VAL B 266 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 277 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP B 268 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 635 " --> pdb=" O THR B 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 265 through 270 removed outlier: 6.964A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 265 through 270 removed outlier: 6.774A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1075 hydrogen bonds defined for protein. 3123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 2.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3711 1.33 - 1.46: 5544 1.46 - 1.59: 11210 1.59 - 1.71: 26 1.71 - 1.84: 236 Bond restraints: 20727 Sorted by residual: bond pdb=" O4P CPL B 807 " pdb=" P CPL B 807 " ideal model delta sigma weight residual 1.648 1.843 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" O4P CPL A 806 " pdb=" P CPL A 806 " ideal model delta sigma weight residual 1.648 1.840 -0.192 2.00e-02 2.50e+03 9.17e+01 bond pdb=" O4P CPL D 802 " pdb=" P CPL D 802 " ideal model delta sigma weight residual 1.648 1.839 -0.191 2.00e-02 2.50e+03 9.09e+01 bond pdb=" O4P CPL D 801 " pdb=" P CPL D 801 " ideal model delta sigma weight residual 1.648 1.838 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" C2 CPL D 801 " pdb=" C3 CPL D 801 " ideal model delta sigma weight residual 1.511 1.643 -0.132 2.00e-02 2.50e+03 4.33e+01 ... (remaining 20722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 27605 3.04 - 6.08: 414 6.08 - 9.12: 61 9.12 - 12.15: 31 12.15 - 15.19: 4 Bond angle restraints: 28115 Sorted by residual: angle pdb=" O3P CPL A 806 " pdb=" P CPL A 806 " pdb=" O4P CPL A 806 " ideal model delta sigma weight residual 93.29 108.48 -15.19 3.00e+00 1.11e-01 2.56e+01 angle pdb=" O3P CPL D 801 " pdb=" P CPL D 801 " pdb=" O4P CPL D 801 " ideal model delta sigma weight residual 93.29 108.42 -15.13 3.00e+00 1.11e-01 2.54e+01 angle pdb=" O3P CPL D 802 " pdb=" P CPL D 802 " pdb=" O4P CPL D 802 " ideal model delta sigma weight residual 93.29 108.04 -14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" O3P CPL B 807 " pdb=" P CPL B 807 " pdb=" O4P CPL B 807 " ideal model delta sigma weight residual 93.29 107.82 -14.53 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C SER D 226 " pdb=" N ASP D 227 " pdb=" CA ASP D 227 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.33e+01 ... (remaining 28110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 12289 35.32 - 70.64: 407 70.64 - 105.95: 33 105.95 - 141.27: 6 141.27 - 176.59: 11 Dihedral angle restraints: 12746 sinusoidal: 5626 harmonic: 7120 Sorted by residual: dihedral pdb=" CA GLN B 310 " pdb=" C GLN B 310 " pdb=" N THR B 311 " pdb=" CA THR B 311 " ideal model delta harmonic sigma weight residual -180.00 -153.47 -26.53 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" N CPL D 802 " pdb=" C4 CPL D 802 " pdb=" C5 CPL D 802 " pdb=" O4P CPL D 802 " ideal model delta sinusoidal sigma weight residual -71.08 105.51 -176.59 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A 806 " pdb=" C1 CPL A 806 " pdb=" C2 CPL A 806 " pdb=" O3P CPL A 806 " ideal model delta sinusoidal sigma weight residual 72.09 -112.97 -174.94 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2843 0.076 - 0.152: 288 0.152 - 0.228: 46 0.228 - 0.303: 4 0.303 - 0.379: 4 Chirality restraints: 3185 Sorted by residual: chirality pdb=" C2 CPL D 802 " pdb=" C1 CPL D 802 " pdb=" C3 CPL D 802 " pdb=" O2 CPL D 802 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" C2 CPL A 806 " pdb=" C1 CPL A 806 " pdb=" C3 CPL A 806 " pdb=" O2 CPL A 806 " both_signs ideal model delta sigma weight residual False -2.32 -2.68 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C2 CPL D 801 " pdb=" C1 CPL D 801 " pdb=" C3 CPL D 801 " pdb=" O2 CPL D 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 3182 not shown) Planarity restraints: 3466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 ERG B 806 " -0.106 2.00e-02 2.50e+03 2.50e-01 6.23e+02 pdb=" C22 ERG B 806 " 0.343 2.00e-02 2.50e+03 pdb=" C23 ERG B 806 " -0.334 2.00e-02 2.50e+03 pdb=" C24 ERG B 806 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG C 805 " 0.220 2.00e-02 2.50e+03 2.33e-01 5.44e+02 pdb=" C22 ERG C 805 " -0.189 2.00e-02 2.50e+03 pdb=" C23 ERG C 805 " -0.274 2.00e-02 2.50e+03 pdb=" C24 ERG C 805 " 0.243 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C20 ERG D 803 " -0.096 2.00e-02 2.50e+03 2.25e-01 5.06e+02 pdb=" C22 ERG D 803 " 0.301 2.00e-02 2.50e+03 pdb=" C23 ERG D 803 " -0.304 2.00e-02 2.50e+03 pdb=" C24 ERG D 803 " 0.100 2.00e-02 2.50e+03 ... (remaining 3463 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4359 2.78 - 3.31: 18248 3.31 - 3.84: 34199 3.84 - 4.37: 39361 4.37 - 4.90: 67586 Nonbonded interactions: 163753 Sorted by model distance: nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.253 3.040 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.271 3.040 nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.274 3.040 nonbonded pdb=" OE1 GLN B 267 " pdb=" OG SER B 275 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.304 3.040 ... (remaining 163748 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 637 or resid 804)) selection = (chain 'B' and (resid 29 through 637 or resid 804)) selection = (chain 'C' and (resid 29 through 637 or resid 804)) selection = (chain 'D' and (resid 29 through 637 or resid 804)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.120 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.195 20727 Z= 0.421 Angle : 0.982 15.192 28115 Z= 0.495 Chirality : 0.051 0.379 3185 Planarity : 0.012 0.250 3466 Dihedral : 18.133 176.591 8146 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 18.50 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.14), residues: 2428 helix: -1.15 (0.11), residues: 1464 sheet: -2.22 (0.40), residues: 124 loop : -1.35 (0.19), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 75 TYR 0.038 0.002 TYR D 621 PHE 0.042 0.002 PHE B 611 TRP 0.053 0.002 TRP C 583 HIS 0.006 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.42 (20727) covalent geometry : angle 0.98217 / 0.50 (28115) hydrogen bonds : bond 0.16036 / 10.71 ( 1075) hydrogen bonds : angle 6.15913 / 4.32 ( 3123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8944 (mptt) cc_final: 0.8578 (mptt) REVERT: A 216 TYR cc_start: 0.7929 (t80) cc_final: 0.7465 (t80) REVERT: B 189 ILE cc_start: 0.9318 (pt) cc_final: 0.9117 (mt) REVERT: B 286 TRP cc_start: 0.7522 (t60) cc_final: 0.7208 (t60) REVERT: B 474 MET cc_start: 0.6651 (ptt) cc_final: 0.6018 (mpp) REVERT: C 100 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8323 (mt-10) REVERT: C 169 PHE cc_start: 0.8867 (m-80) cc_final: 0.8585 (m-10) REVERT: C 218 LEU cc_start: 0.8352 (tp) cc_final: 0.7778 (tt) REVERT: C 222 TYR cc_start: 0.7831 (m-80) cc_final: 0.7455 (m-80) REVERT: C 589 ARG cc_start: 0.7552 (ptp90) cc_final: 0.7349 (ptt90) REVERT: D 389 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7389 (mt-10) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1534 time to fit residues: 83.4816 Evaluate side-chains 304 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 306 GLN C 380 HIS ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.154185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120861 restraints weight = 28403.304| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.17 r_work: 0.3376 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20727 Z= 0.120 Angle : 0.585 10.720 28115 Z= 0.282 Chirality : 0.039 0.272 3185 Planarity : 0.004 0.056 3466 Dihedral : 13.969 179.808 3534 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.09 % Allowed : 17.27 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.16), residues: 2428 helix: 0.33 (0.13), residues: 1516 sheet: -2.07 (0.40), residues: 124 loop : -0.70 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 414 TYR 0.015 0.001 TYR C 555 PHE 0.020 0.001 PHE C 211 TRP 0.022 0.001 TRP C 583 HIS 0.004 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (20727) covalent geometry : angle 0.58548 / 0.28 (28115) hydrogen bonds : bond 0.03927 / 2.63 ( 1075) hydrogen bonds : angle 4.11178 / 2.91 ( 3123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 323 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8426 (ttt90) cc_final: 0.7817 (ttp-110) REVERT: A 62 LYS cc_start: 0.8947 (mttt) cc_final: 0.8543 (mmmt) REVERT: A 108 GLU cc_start: 0.7666 (tp30) cc_final: 0.7402 (tp30) REVERT: A 210 THR cc_start: 0.7973 (p) cc_final: 0.7704 (t) REVERT: A 216 TYR cc_start: 0.7964 (t80) cc_final: 0.7590 (t80) REVERT: A 315 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: A 377 TYR cc_start: 0.7887 (m-80) cc_final: 0.7666 (m-10) REVERT: A 389 GLU cc_start: 0.7913 (tt0) cc_final: 0.7696 (tt0) REVERT: A 491 MET cc_start: 0.8503 (mmp) cc_final: 0.7483 (ttp) REVERT: B 59 ARG cc_start: 0.8643 (ptm-80) cc_final: 0.8403 (ptm-80) REVERT: B 440 MET cc_start: 0.8698 (tmm) cc_final: 0.8443 (tmm) REVERT: B 474 MET cc_start: 0.6674 (ptt) cc_final: 0.6125 (mpp) REVERT: B 522 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: C 589 ARG cc_start: 0.7775 (ptp90) cc_final: 0.7411 (ptt90) REVERT: D 193 ASP cc_start: 0.7141 (t0) cc_final: 0.6860 (t0) REVERT: D 306 GLN cc_start: 0.8574 (mm-40) cc_final: 0.7948 (mp10) REVERT: D 389 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7315 (mt-10) outliers start: 44 outliers final: 25 residues processed: 352 average time/residue: 0.1515 time to fit residues: 82.5716 Evaluate side-chains 319 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 292 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 13 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 209 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 219 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 165 HIS B 225 HIS C 74 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 GLN D 185 HIS D 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111892 restraints weight = 28840.028| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.19 r_work: 0.3258 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20727 Z= 0.233 Angle : 0.670 10.744 28115 Z= 0.323 Chirality : 0.043 0.265 3185 Planarity : 0.004 0.056 3466 Dihedral : 13.444 179.581 3534 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.42 % Allowed : 17.13 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.17), residues: 2428 helix: 0.72 (0.13), residues: 1516 sheet: -1.98 (0.41), residues: 124 loop : -0.56 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 363 TYR 0.016 0.002 TYR A 555 PHE 0.020 0.002 PHE C 211 TRP 0.014 0.001 TRP C 286 HIS 0.007 0.001 HIS A 582 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.23 (20727) covalent geometry : angle 0.67023 / 0.32 (28115) hydrogen bonds : bond 0.04340 / 2.89 ( 1075) hydrogen bonds : angle 4.13847 / 2.92 ( 3123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 35 ARG cc_start: 0.8546 (ttt90) cc_final: 0.7901 (ttp-110) REVERT: A 62 LYS cc_start: 0.8930 (mttt) cc_final: 0.8521 (mmmt) REVERT: A 108 GLU cc_start: 0.7760 (tp30) cc_final: 0.7486 (tp30) REVERT: A 216 TYR cc_start: 0.8082 (t80) cc_final: 0.7734 (t80) REVERT: A 315 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: A 389 GLU cc_start: 0.8096 (tt0) cc_final: 0.7767 (tt0) REVERT: A 491 MET cc_start: 0.8735 (mmp) cc_final: 0.7554 (ttp) REVERT: A 540 ILE cc_start: 0.8987 (tp) cc_final: 0.8718 (tp) REVERT: B 217 ASN cc_start: 0.8633 (t0) cc_final: 0.8405 (m-40) REVERT: B 440 MET cc_start: 0.8716 (tmm) cc_final: 0.8462 (tmm) REVERT: B 474 MET cc_start: 0.7010 (ptt) cc_final: 0.6588 (mpp) REVERT: B 522 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: B 578 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7620 (mtm) REVERT: C 589 ARG cc_start: 0.7784 (ptp90) cc_final: 0.7339 (ptt90) REVERT: D 193 ASP cc_start: 0.7523 (t0) cc_final: 0.7210 (t0) REVERT: D 216 TYR cc_start: 0.8501 (t80) cc_final: 0.7291 (t80) REVERT: D 259 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8269 (mm) REVERT: D 306 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8087 (mp10) outliers start: 72 outliers final: 46 residues processed: 345 average time/residue: 0.1324 time to fit residues: 71.1771 Evaluate side-chains 328 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 278 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 112 CYS Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 347 CYS Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 500 VAL Chi-restraints excluded: chain D residue 597 VAL Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 231 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 165 optimal weight: 0.9980 chunk 227 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116395 restraints weight = 28713.987| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.21 r_work: 0.3293 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20727 Z= 0.112 Angle : 0.553 11.021 28115 Z= 0.264 Chirality : 0.039 0.281 3185 Planarity : 0.004 0.059 3466 Dihedral : 13.063 177.074 3534 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.28 % Allowed : 19.26 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2428 helix: 1.15 (0.13), residues: 1520 sheet: -2.00 (0.41), residues: 124 loop : -0.45 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 594 TYR 0.017 0.001 TYR D 621 PHE 0.021 0.001 PHE C 611 TRP 0.010 0.001 TRP C 583 HIS 0.012 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (20727) covalent geometry : angle 0.55294 / 0.26 (28115) hydrogen bonds : bond 0.03515 / 2.35 ( 1075) hydrogen bonds : angle 3.86456 / 2.73 ( 3123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 304 time to evaluate : 0.776 Fit side-chains REVERT: A 35 ARG cc_start: 0.8462 (ttt90) cc_final: 0.7806 (ttp-110) REVERT: A 62 LYS cc_start: 0.8892 (mttt) cc_final: 0.8504 (mmmt) REVERT: A 93 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: A 108 GLU cc_start: 0.7684 (tp30) cc_final: 0.7403 (tp30) REVERT: A 216 TYR cc_start: 0.7840 (t80) cc_final: 0.7637 (t80) REVERT: A 315 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: A 389 GLU cc_start: 0.8130 (tt0) cc_final: 0.7590 (mt-10) REVERT: A 491 MET cc_start: 0.8541 (mmp) cc_final: 0.7384 (ttp) REVERT: A 540 ILE cc_start: 0.8954 (tp) cc_final: 0.8677 (tp) REVERT: B 440 MET cc_start: 0.8656 (tmm) cc_final: 0.8238 (tmm) REVERT: B 474 MET cc_start: 0.6927 (ptt) cc_final: 0.6491 (mpp) REVERT: B 522 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: B 578 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7560 (ttp) REVERT: C 501 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8081 (mm) REVERT: C 589 ARG cc_start: 0.7723 (ptp90) cc_final: 0.7230 (ptt90) REVERT: D 193 ASP cc_start: 0.7310 (t0) cc_final: 0.6977 (t0) REVERT: D 216 TYR cc_start: 0.8424 (t80) cc_final: 0.8192 (t80) REVERT: D 219 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8856 (mm) REVERT: D 306 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7899 (mp10) REVERT: D 403 GLU cc_start: 0.8063 (tp30) cc_final: 0.7632 (tp30) outliers start: 48 outliers final: 26 residues processed: 334 average time/residue: 0.1429 time to fit residues: 74.5116 Evaluate side-chains 308 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 276 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 120 optimal weight: 10.0000 chunk 237 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 127 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 483 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.115857 restraints weight = 28371.033| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.23 r_work: 0.3308 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20727 Z= 0.112 Angle : 0.546 10.906 28115 Z= 0.260 Chirality : 0.038 0.277 3185 Planarity : 0.004 0.058 3466 Dihedral : 12.875 176.041 3534 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.08 % Allowed : 18.60 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2428 helix: 1.35 (0.13), residues: 1524 sheet: -2.00 (0.41), residues: 124 loop : -0.32 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 615 TYR 0.016 0.001 TYR C 415 PHE 0.022 0.001 PHE C 211 TRP 0.010 0.001 TRP C 286 HIS 0.008 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (20727) covalent geometry : angle 0.54586 / 0.26 (28115) hydrogen bonds : bond 0.03407 / 2.27 ( 1075) hydrogen bonds : angle 3.78611 / 2.68 ( 3123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 294 time to evaluate : 0.743 Fit side-chains REVERT: A 35 ARG cc_start: 0.8428 (ttt90) cc_final: 0.7799 (ttp-170) REVERT: A 62 LYS cc_start: 0.8887 (mttt) cc_final: 0.8481 (mmmt) REVERT: A 93 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: A 108 GLU cc_start: 0.7640 (tp30) cc_final: 0.7357 (tp30) REVERT: A 195 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8266 (tt) REVERT: A 389 GLU cc_start: 0.8053 (tt0) cc_final: 0.7648 (mt-10) REVERT: A 491 MET cc_start: 0.8509 (mmp) cc_final: 0.7321 (ttp) REVERT: A 540 ILE cc_start: 0.8964 (tp) cc_final: 0.8699 (tp) REVERT: B 217 ASN cc_start: 0.8624 (t0) cc_final: 0.8387 (m-40) REVERT: B 440 MET cc_start: 0.8669 (tmm) cc_final: 0.8464 (tmm) REVERT: B 474 MET cc_start: 0.6822 (ptt) cc_final: 0.6431 (mpp) REVERT: B 522 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: B 578 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7415 (mtm) REVERT: C 169 PHE cc_start: 0.9009 (m-80) cc_final: 0.8722 (m-10) REVERT: C 491 MET cc_start: 0.8967 (mmm) cc_final: 0.8710 (mmm) REVERT: C 589 ARG cc_start: 0.7666 (ptp90) cc_final: 0.7247 (ptt90) REVERT: C 615 ARG cc_start: 0.7274 (ttt180) cc_final: 0.6523 (mmm160) REVERT: D 193 ASP cc_start: 0.7268 (t0) cc_final: 0.6930 (t0) REVERT: D 216 TYR cc_start: 0.8385 (t80) cc_final: 0.8184 (t80) REVERT: D 306 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7910 (mp10) REVERT: D 403 GLU cc_start: 0.8158 (tp30) cc_final: 0.7891 (tp30) outliers start: 65 outliers final: 35 residues processed: 337 average time/residue: 0.1403 time to fit residues: 74.4781 Evaluate side-chains 318 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 235 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 159 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.114339 restraints weight = 28474.792| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.17 r_work: 0.3286 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20727 Z= 0.155 Angle : 0.595 10.930 28115 Z= 0.282 Chirality : 0.040 0.279 3185 Planarity : 0.004 0.058 3466 Dihedral : 12.891 175.316 3534 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.99 % Allowed : 19.12 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.17), residues: 2428 helix: 1.39 (0.13), residues: 1504 sheet: -2.04 (0.40), residues: 124 loop : -0.32 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 615 TYR 0.020 0.001 TYR C 415 PHE 0.023 0.001 PHE C 611 TRP 0.011 0.001 TRP C 286 HIS 0.007 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (20727) covalent geometry : angle 0.59484 / 0.28 (28115) hydrogen bonds : bond 0.03706 / 2.47 ( 1075) hydrogen bonds : angle 3.90380 / 2.77 ( 3123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 284 time to evaluate : 0.521 Fit side-chains REVERT: A 35 ARG cc_start: 0.8537 (ttt90) cc_final: 0.7876 (ttp-110) REVERT: A 62 LYS cc_start: 0.8872 (mttt) cc_final: 0.8466 (pttt) REVERT: A 93 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: A 108 GLU cc_start: 0.7636 (tp30) cc_final: 0.7373 (tp30) REVERT: A 216 TYR cc_start: 0.7925 (t80) cc_final: 0.7654 (t80) REVERT: A 389 GLU cc_start: 0.8045 (tt0) cc_final: 0.7624 (mt-10) REVERT: A 540 ILE cc_start: 0.9009 (tp) cc_final: 0.8696 (tp) REVERT: B 315 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: B 440 MET cc_start: 0.8692 (tmm) cc_final: 0.8265 (tmm) REVERT: B 474 MET cc_start: 0.6866 (ptt) cc_final: 0.6494 (mpp) REVERT: B 522 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: B 629 TRP cc_start: 0.8355 (m100) cc_final: 0.7644 (m100) REVERT: C 589 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7312 (ptt90) REVERT: C 615 ARG cc_start: 0.7159 (ttt180) cc_final: 0.6563 (mmm160) REVERT: D 193 ASP cc_start: 0.7474 (t0) cc_final: 0.7169 (t0) REVERT: D 216 TYR cc_start: 0.8363 (t80) cc_final: 0.8095 (t80) REVERT: D 259 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8271 (mm) REVERT: D 306 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8025 (mp10) REVERT: D 403 GLU cc_start: 0.8316 (tp30) cc_final: 0.7986 (tp30) outliers start: 63 outliers final: 45 residues processed: 329 average time/residue: 0.1372 time to fit residues: 70.9467 Evaluate side-chains 322 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 273 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 347 CYS Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 524 SER Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 46 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 8 optimal weight: 0.0070 chunk 235 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 208 optimal weight: 0.9990 chunk 72 optimal weight: 0.0270 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.151657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.118238 restraints weight = 28475.794| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.20 r_work: 0.3317 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20727 Z= 0.103 Angle : 0.562 11.101 28115 Z= 0.263 Chirality : 0.038 0.285 3185 Planarity : 0.004 0.057 3466 Dihedral : 12.668 174.338 3534 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.56 % Allowed : 19.92 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.17), residues: 2428 helix: 1.54 (0.13), residues: 1504 sheet: -2.04 (0.39), residues: 124 loop : -0.23 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 632 TYR 0.022 0.001 TYR C 415 PHE 0.019 0.001 PHE C 574 TRP 0.008 0.001 TRP D 286 HIS 0.007 0.000 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (20727) covalent geometry : angle 0.56158 / 0.26 (28115) hydrogen bonds : bond 0.03301 / 2.21 ( 1075) hydrogen bonds : angle 3.78510 / 2.69 ( 3123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.782 Fit side-chains REVERT: A 35 ARG cc_start: 0.8477 (ttt90) cc_final: 0.7832 (ttp-170) REVERT: A 62 LYS cc_start: 0.8923 (mttt) cc_final: 0.8436 (pttt) REVERT: A 65 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8018 (pp) REVERT: A 93 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8134 (mm-30) REVERT: A 108 GLU cc_start: 0.7638 (tp30) cc_final: 0.7350 (tp30) REVERT: A 216 TYR cc_start: 0.7797 (t80) cc_final: 0.7545 (t80) REVERT: A 315 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8240 (mp0) REVERT: A 389 GLU cc_start: 0.8014 (tt0) cc_final: 0.7675 (mt-10) REVERT: A 491 MET cc_start: 0.8565 (mmp) cc_final: 0.7332 (ttp) REVERT: A 540 ILE cc_start: 0.8982 (tp) cc_final: 0.8767 (tp) REVERT: B 112 CYS cc_start: 0.6323 (m) cc_final: 0.5920 (m) REVERT: B 474 MET cc_start: 0.6867 (ptt) cc_final: 0.6398 (mpp) REVERT: B 522 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8465 (mt-10) REVERT: B 629 TRP cc_start: 0.8243 (m100) cc_final: 0.7594 (m100) REVERT: C 169 PHE cc_start: 0.9009 (m-80) cc_final: 0.8763 (m-10) REVERT: C 222 TYR cc_start: 0.8028 (m-80) cc_final: 0.7646 (m-80) REVERT: C 491 MET cc_start: 0.8964 (mmm) cc_final: 0.8704 (mmm) REVERT: C 554 MET cc_start: 0.7451 (tpp) cc_final: 0.7230 (tpp) REVERT: C 589 ARG cc_start: 0.7825 (ptp90) cc_final: 0.7387 (ptt90) REVERT: D 193 ASP cc_start: 0.7234 (t0) cc_final: 0.6919 (t0) REVERT: D 216 TYR cc_start: 0.8483 (t80) cc_final: 0.7878 (t80) REVERT: D 306 GLN cc_start: 0.8515 (mm-40) cc_final: 0.7893 (mp10) REVERT: D 403 GLU cc_start: 0.8209 (tp30) cc_final: 0.7901 (tp30) outliers start: 54 outliers final: 37 residues processed: 335 average time/residue: 0.1412 time to fit residues: 74.7957 Evaluate side-chains 319 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 36 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 164 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 127 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 HIS B 310 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.153474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120332 restraints weight = 28440.353| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.20 r_work: 0.3343 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20727 Z= 0.106 Angle : 0.581 11.219 28115 Z= 0.271 Chirality : 0.038 0.304 3185 Planarity : 0.004 0.055 3466 Dihedral : 12.487 172.459 3534 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.47 % Allowed : 20.07 % Favored : 77.47 % 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 are not related in a simple way. whole: 1.18 (0.17), residues: 2428 helix: 1.59 (0.13), residues: 1496 sheet: -1.98 (0.40), residues: 124 loop : -0.17 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 615 TYR 0.015 0.001 TYR D 621 PHE 0.023 0.001 PHE C 611 TRP 0.012 0.001 TRP C 286 HIS 0.006 0.001 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (20727) covalent geometry : angle 0.58077 / 0.27 (28115) hydrogen bonds : bond 0.03291 / 2.19 ( 1075) hydrogen bonds : angle 3.76033 / 2.67 ( 3123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 295 time to evaluate : 0.778 Fit side-chains REVERT: A 35 ARG cc_start: 0.8550 (ttt90) cc_final: 0.7899 (ttp-170) REVERT: A 59 ARG cc_start: 0.8459 (tmm-80) cc_final: 0.8124 (ttp-110) REVERT: A 62 LYS cc_start: 0.8879 (mttt) cc_final: 0.8428 (pttt) REVERT: A 108 GLU cc_start: 0.7651 (tp30) cc_final: 0.7390 (tp30) REVERT: A 315 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: A 389 GLU cc_start: 0.8005 (tt0) cc_final: 0.7659 (mt-10) REVERT: A 491 MET cc_start: 0.8577 (mmp) cc_final: 0.7259 (ttp) REVERT: A 540 ILE cc_start: 0.8971 (tp) cc_final: 0.8748 (tp) REVERT: B 112 CYS cc_start: 0.6332 (m) cc_final: 0.5951 (m) REVERT: B 474 MET cc_start: 0.6767 (ptt) cc_final: 0.6444 (mpp) REVERT: B 522 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8424 (mt-10) REVERT: B 629 TRP cc_start: 0.8234 (m100) cc_final: 0.7632 (m100) REVERT: C 169 PHE cc_start: 0.9066 (m-80) cc_final: 0.8814 (m-10) REVERT: C 222 TYR cc_start: 0.7998 (m-80) cc_final: 0.7665 (m-80) REVERT: C 491 MET cc_start: 0.8951 (mmm) cc_final: 0.8678 (mmm) REVERT: C 589 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7604 (ptt-90) REVERT: D 193 ASP cc_start: 0.7335 (t0) cc_final: 0.7046 (t0) REVERT: D 216 TYR cc_start: 0.8479 (t80) cc_final: 0.7926 (t80) REVERT: D 306 GLN cc_start: 0.8521 (mm-40) cc_final: 0.7936 (mp10) REVERT: D 403 GLU cc_start: 0.8250 (tp30) cc_final: 0.7956 (tp30) REVERT: D 625 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6605 (mm) outliers start: 52 outliers final: 41 residues processed: 329 average time/residue: 0.1385 time to fit residues: 72.1999 Evaluate side-chains 326 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 282 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 540 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 166 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 76 optimal weight: 0.0270 chunk 147 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 59 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.155316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122411 restraints weight = 28101.608| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.17 r_work: 0.3373 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20727 Z= 0.103 Angle : 0.580 11.685 28115 Z= 0.270 Chirality : 0.038 0.317 3185 Planarity : 0.004 0.055 3466 Dihedral : 12.352 171.287 3534 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.23 % Allowed : 20.68 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.17), residues: 2428 helix: 1.63 (0.13), residues: 1496 sheet: -1.94 (0.39), residues: 124 loop : -0.15 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 615 TYR 0.023 0.001 TYR C 415 PHE 0.023 0.001 PHE C 211 TRP 0.009 0.001 TRP C 286 HIS 0.006 0.000 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (20727) covalent geometry : angle 0.58018 / 0.27 (28115) hydrogen bonds : bond 0.03215 / 2.14 ( 1075) hydrogen bonds : angle 3.73503 / 2.65 ( 3123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 296 time to evaluate : 0.635 Fit side-chains REVERT: A 35 ARG cc_start: 0.8518 (ttt90) cc_final: 0.7872 (ttp-170) REVERT: A 62 LYS cc_start: 0.8878 (mttt) cc_final: 0.8443 (pttt) REVERT: A 108 GLU cc_start: 0.7647 (tp30) cc_final: 0.7394 (tp30) REVERT: A 216 TYR cc_start: 0.7421 (t80) cc_final: 0.7069 (t80) REVERT: A 389 GLU cc_start: 0.7944 (tt0) cc_final: 0.7625 (mt-10) REVERT: A 491 MET cc_start: 0.8564 (mmp) cc_final: 0.7229 (ttp) REVERT: A 540 ILE cc_start: 0.8903 (tp) cc_final: 0.8690 (tp) REVERT: A 578 MET cc_start: 0.8381 (mmt) cc_final: 0.8065 (mmt) REVERT: B 112 CYS cc_start: 0.6317 (m) cc_final: 0.5969 (m) REVERT: B 474 MET cc_start: 0.6682 (ptt) cc_final: 0.6393 (mpp) REVERT: B 522 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: B 629 TRP cc_start: 0.8242 (m100) cc_final: 0.7658 (m100) REVERT: C 169 PHE cc_start: 0.9057 (m-80) cc_final: 0.8789 (m-10) REVERT: C 222 TYR cc_start: 0.8008 (m-80) cc_final: 0.7646 (m-80) REVERT: C 491 MET cc_start: 0.8898 (mmm) cc_final: 0.8658 (mmm) REVERT: C 589 ARG cc_start: 0.7828 (ptp90) cc_final: 0.7570 (ptt-90) REVERT: D 193 ASP cc_start: 0.7285 (t0) cc_final: 0.7031 (t0) REVERT: D 216 TYR cc_start: 0.8296 (t80) cc_final: 0.7292 (t80) REVERT: D 259 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8275 (mm) REVERT: D 306 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7871 (mp10) REVERT: D 403 GLU cc_start: 0.8189 (tp30) cc_final: 0.7945 (tp30) REVERT: D 625 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6624 (mm) outliers start: 47 outliers final: 36 residues processed: 325 average time/residue: 0.1356 time to fit residues: 70.3267 Evaluate side-chains 324 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 285 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 625 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 92 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 34 optimal weight: 0.0040 chunk 107 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 184 optimal weight: 0.5980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.154863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.121810 restraints weight = 28518.106| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.19 r_work: 0.3368 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20727 Z= 0.105 Angle : 0.588 12.583 28115 Z= 0.271 Chirality : 0.038 0.322 3185 Planarity : 0.004 0.054 3466 Dihedral : 12.265 170.659 3534 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.18 % Allowed : 21.30 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.17), residues: 2428 helix: 1.66 (0.13), residues: 1504 sheet: -1.90 (0.39), residues: 124 loop : -0.17 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 632 TYR 0.026 0.001 TYR D 415 PHE 0.027 0.001 PHE C 611 TRP 0.007 0.001 TRP A 593 HIS 0.006 0.000 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (20727) covalent geometry : angle 0.58836 / 0.27 (28115) hydrogen bonds : bond 0.03176 / 2.13 ( 1075) hydrogen bonds : angle 3.72606 / 2.65 ( 3123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 286 time to evaluate : 0.789 Fit side-chains REVERT: A 35 ARG cc_start: 0.8482 (ttt90) cc_final: 0.7830 (ttp-110) REVERT: A 62 LYS cc_start: 0.8906 (mttt) cc_final: 0.8473 (pttt) REVERT: A 108 GLU cc_start: 0.7622 (tp30) cc_final: 0.7379 (tp30) REVERT: A 389 GLU cc_start: 0.7957 (tt0) cc_final: 0.7652 (mt-10) REVERT: A 491 MET cc_start: 0.8491 (mmp) cc_final: 0.7137 (ttp) REVERT: A 540 ILE cc_start: 0.8922 (tp) cc_final: 0.8694 (tp) REVERT: B 97 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8664 (tt) REVERT: B 112 CYS cc_start: 0.6283 (m) cc_final: 0.5936 (m) REVERT: B 185 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8488 (t-90) REVERT: B 474 MET cc_start: 0.6727 (ptt) cc_final: 0.6417 (mpp) REVERT: B 522 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8382 (mt-10) REVERT: B 629 TRP cc_start: 0.8255 (m100) cc_final: 0.7770 (m100) REVERT: C 169 PHE cc_start: 0.9050 (m-80) cc_final: 0.8772 (m-10) REVERT: C 222 TYR cc_start: 0.8006 (m-80) cc_final: 0.7641 (m-80) REVERT: C 286 TRP cc_start: 0.7187 (t60) cc_final: 0.6949 (t60) REVERT: C 491 MET cc_start: 0.8925 (mmm) cc_final: 0.8676 (mmm) REVERT: C 589 ARG cc_start: 0.7894 (ptp90) cc_final: 0.7592 (ptt-90) REVERT: D 193 ASP cc_start: 0.7298 (t0) cc_final: 0.7042 (t0) REVERT: D 216 TYR cc_start: 0.8395 (t80) cc_final: 0.7380 (t80) REVERT: D 306 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7867 (mp10) REVERT: D 403 GLU cc_start: 0.8238 (tp30) cc_final: 0.7981 (tp30) REVERT: D 554 MET cc_start: 0.8378 (tpp) cc_final: 0.7906 (tpp) outliers start: 46 outliers final: 38 residues processed: 316 average time/residue: 0.1342 time to fit residues: 67.6033 Evaluate side-chains 323 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 282 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 637 HIS Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 185 HIS Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 522 GLU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain C residue 44 ILE Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 294 GLU Chi-restraints excluded: chain C residue 364 ASP Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 286 TRP Chi-restraints excluded: chain D residue 307 ILE Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 447 MET Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 89 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 99 optimal weight: 0.0170 chunk 43 optimal weight: 0.7980 chunk 142 optimal weight: 0.0670 chunk 179 optimal weight: 0.0770 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 582 HIS B 519 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.125142 restraints weight = 28395.665| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.23 r_work: 0.3410 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 20727 Z= 0.101 Angle : 0.581 12.768 28115 Z= 0.269 Chirality : 0.038 0.329 3185 Planarity : 0.004 0.054 3466 Dihedral : 12.138 169.898 3534 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.04 % Allowed : 21.54 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.17), residues: 2428 helix: 1.73 (0.13), residues: 1488 sheet: -1.87 (0.39), residues: 124 loop : -0.08 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 594 TYR 0.024 0.001 TYR D 415 PHE 0.024 0.001 PHE C 211 TRP 0.009 0.001 TRP A 593 HIS 0.006 0.000 HIS A 258 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (20727) covalent geometry : angle 0.58103 / 0.27 (28115) hydrogen bonds : bond 0.03115 / 2.08 ( 1075) hydrogen bonds : angle 3.72127 / 2.65 ( 3123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4982.05 seconds wall clock time: 86 minutes 12.96 seconds (5172.96 seconds total)