Starting phenix.real_space_refine on Thu Sep 18 16:58:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e24_47433/09_2025/9e24_47433.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e24_47433/09_2025/9e24_47433.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e24_47433/09_2025/9e24_47433.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e24_47433/09_2025/9e24_47433.map" model { file = "/net/cci-nas-00/data/ceres_data/9e24_47433/09_2025/9e24_47433.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e24_47433/09_2025/9e24_47433.cif" } resolution = 3.4 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 11334 2.51 5 N 3402 2.21 5 O 3486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18324 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Chain: "F" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3054 Classifications: {'peptide': 422} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 17, 'TRANS': 404} Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 5.29, per 1000 atoms: 0.29 Number of scatterers: 18324 At special positions: 0 Unit cell: (124.63, 134.93, 98.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3486 8.00 N 3402 7.00 C 11334 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: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.9 microseconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4644 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 12 sheets defined 45.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.921A pdb=" N ALA A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 106 through 126 removed outlier: 3.786A pdb=" N ILE A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 removed outlier: 3.726A pdb=" N HIS A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.339A pdb=" N LEU A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 202 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 337 through 346 Processing helix chain 'A' and resid 361 through 372 removed outlier: 4.073A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 480 through 488 Processing helix chain 'A' and resid 489 through 500 Processing helix chain 'B' and resid 81 through 97 removed outlier: 3.606A pdb=" N THR B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN B 91 " --> pdb=" O THR B 87 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ALA B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 94 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN B 95 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 104 Processing helix chain 'B' and resid 107 through 126 removed outlier: 4.047A pdb=" N GLY B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 147 Processing helix chain 'B' and resid 150 through 157 removed outlier: 4.356A pdb=" N LEU B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.587A pdb=" N ALA B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.796A pdb=" N ARG B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 4.077A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 400 Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 487 removed outlier: 3.533A pdb=" N ALA B 484 " --> pdb=" O PHE B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'C' and resid 81 through 97 removed outlier: 3.775A pdb=" N ILE C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.780A pdb=" N LEU C 102 " --> pdb=" O ASP C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 126 removed outlier: 3.583A pdb=" N GLU C 113 " --> pdb=" O GLN C 109 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP C 116 " --> pdb=" O GLU C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 146 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.716A pdb=" N GLN C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.562A pdb=" N LEU C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.578A pdb=" N ALA C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.813A pdb=" N ARG C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 removed outlier: 3.950A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 399 Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 489 through 501 removed outlier: 4.392A pdb=" N GLU C 501 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 103 removed outlier: 3.526A pdb=" N ALA D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 126 Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 156 Processing helix chain 'D' and resid 188 through 202 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.734A pdb=" N ARG D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.017A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 405 through 417 Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'E' and resid 81 through 97 removed outlier: 4.145A pdb=" N THR E 85 " --> pdb=" O TYR E 81 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN E 91 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA E 92 " --> pdb=" O THR E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 Processing helix chain 'E' and resid 107 through 126 removed outlier: 4.282A pdb=" N GLY E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 147 Processing helix chain 'E' and resid 150 through 157 removed outlier: 4.342A pdb=" N LEU E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 286 through 296 Processing helix chain 'E' and resid 337 through 347 removed outlier: 3.752A pdb=" N ARG E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 372 removed outlier: 3.857A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 368 " --> pdb=" O PHE E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.547A pdb=" N SER E 391 " --> pdb=" O ARG E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 487 removed outlier: 3.554A pdb=" N ALA E 484 " --> pdb=" O PHE E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 500 Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 103 Processing helix chain 'F' and resid 106 through 126 removed outlier: 3.634A pdb=" N GLU F 113 " --> pdb=" O GLN F 109 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASP F 116 " --> pdb=" O GLU F 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 146 removed outlier: 3.985A pdb=" N VAL F 138 " --> pdb=" O GLN F 134 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 157 Processing helix chain 'F' and resid 188 through 202 removed outlier: 3.707A pdb=" N GLN F 202 " --> pdb=" O ARG F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.647A pdb=" N ALA F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 346 removed outlier: 3.532A pdb=" N LEU F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 349 No H-bonds generated for 'chain 'F' and resid 347 through 349' Processing helix chain 'F' and resid 361 through 372 removed outlier: 3.906A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 480 through 488 Processing helix chain 'F' and resid 489 through 501 removed outlier: 4.347A pdb=" N GLU F 501 " --> pdb=" O LEU F 497 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 4.038A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 320 through 324 removed outlier: 6.579A pdb=" N VAL A 304 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 323 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR A 306 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET A 378 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLY A 356 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 380 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS A 382 " --> pdb=" O VAL A 358 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 435 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA A 424 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE A 433 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 17.474A pdb=" N ARG A 431 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 14.151A pdb=" N THR A 458 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 10.563A pdb=" N ILE A 433 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLU A 456 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N HIS A 435 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 454 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR A 437 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 452 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N VAL A 439 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLN A 450 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TYR A 455 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG A 471 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ILE A 457 " --> pdb=" O LYS A 469 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 469 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 459 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 182 removed outlier: 4.520A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 170 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 320 through 324 removed outlier: 6.617A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ILE B 353 " --> pdb=" O MET B 378 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR B 380 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL B 355 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N HIS B 382 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU B 277 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N LEU B 381 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 279 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 278 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA B 423 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA B 424 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ILE B 433 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N ARG B 432 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N GLU B 456 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N THR B 434 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 454 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 436 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 448 " --> pdb=" O VAL B 440 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU B 442 " --> pdb=" O VAL B 446 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TYR B 455 " --> pdb=" O ARG B 471 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG B 471 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE B 457 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS B 469 " --> pdb=" O ILE B 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 178 through 182 removed outlier: 4.453A pdb=" N VAL C 171 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 320 through 322 removed outlier: 6.441A pdb=" N VAL C 304 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU C 277 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU C 381 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 279 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL C 278 " --> pdb=" O ILE C 421 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ALA C 423 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N SER C 280 " --> pdb=" O ALA C 423 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N ARG C 425 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE C 420 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE C 436 " --> pdb=" O ILE C 420 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N ARG C 432 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 10.225A pdb=" N GLU C 456 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR C 434 " --> pdb=" O VAL C 454 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL C 454 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE C 436 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU C 442 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N TYR C 455 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG C 471 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N ILE C 457 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS C 469 " --> pdb=" O ILE C 457 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 178 through 181 removed outlier: 3.843A pdb=" N ASP D 162 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 320 through 324 removed outlier: 6.566A pdb=" N VAL D 304 " --> pdb=" O VAL D 321 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU D 323 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR D 306 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N GLY D 356 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N CYS D 307 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL D 358 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET D 378 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY D 356 " --> pdb=" O MET D 378 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR D 380 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N HIS D 382 " --> pdb=" O VAL D 358 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL D 278 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA D 423 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER D 280 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N ARG D 425 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS D 435 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA D 424 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE D 433 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 17.552A pdb=" N ARG D 431 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 14.173A pdb=" N THR D 458 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 10.685A pdb=" N ILE D 433 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N GLU D 456 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N HIS D 435 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 454 " --> pdb=" O HIS D 435 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR D 437 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU D 452 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N VAL D 439 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN D 450 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR D 455 " --> pdb=" O ARG D 471 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ARG D 471 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ILE D 457 " --> pdb=" O LYS D 469 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS D 469 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 459 " --> pdb=" O VAL D 467 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 178 through 182 removed outlier: 4.567A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG E 170 " --> pdb=" O ASN E 166 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP E 162 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 320 through 324 removed outlier: 6.304A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE E 353 " --> pdb=" O MET E 378 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N THR E 380 " --> pdb=" O ILE E 353 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL E 355 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N HIS E 382 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU E 277 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LEU E 381 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL E 278 " --> pdb=" O ILE E 421 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA E 423 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA E 424 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE E 433 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 11.609A pdb=" N ARG E 432 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N GLU E 456 " --> pdb=" O ARG E 432 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N THR E 434 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL E 454 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE E 436 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL E 448 " --> pdb=" O VAL E 440 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU E 442 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL E 446 " --> pdb=" O LEU E 442 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TYR E 455 " --> pdb=" O ARG E 471 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG E 471 " --> pdb=" O TYR E 455 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE E 457 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS E 469 " --> pdb=" O ILE E 457 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 178 through 182 removed outlier: 4.399A pdb=" N VAL F 171 " --> pdb=" O THR F 182 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 321 through 322 removed outlier: 6.232A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE F 353 " --> pdb=" O MET F 378 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N THR F 380 " --> pdb=" O ILE F 353 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N VAL F 355 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 9.708A pdb=" N HIS F 382 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY F 379 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL F 278 " --> pdb=" O ILE F 421 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA F 423 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N SER F 280 " --> pdb=" O ALA F 423 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG F 425 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 11.577A pdb=" N ARG F 432 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 10.194A pdb=" N GLU F 456 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR F 434 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL F 454 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE F 436 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N TYR F 455 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG F 471 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE F 457 " --> pdb=" O LYS F 469 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS F 469 " --> pdb=" O ILE F 457 " (cutoff:3.500A) 942 hydrogen bonds defined for protein. 2748 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: 3.42 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6522 1.34 - 1.46: 1661 1.46 - 1.57: 10201 1.57 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 18552 Sorted by residual: bond pdb=" CG GLN E 368 " pdb=" CD GLN E 368 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CA ILE F 279 " pdb=" CB ILE F 279 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.28e+00 bond pdb=" CA ILE C 279 " pdb=" CB ILE C 279 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" CB GLN C 316 " pdb=" CG GLN C 316 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.17e+00 bond pdb=" N LEU E 107 " pdb=" CA LEU E 107 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.09e+00 ... (remaining 18547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 24917 1.93 - 3.85: 229 3.85 - 5.78: 25 5.78 - 7.71: 4 7.71 - 9.64: 1 Bond angle restraints: 25176 Sorted by residual: angle pdb=" CB MET F 250 " pdb=" CG MET F 250 " pdb=" SD MET F 250 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA GLN F 316 " pdb=" CB GLN F 316 " pdb=" CG GLN F 316 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.50e+00 angle pdb=" CA GLN C 316 " pdb=" CB GLN C 316 " pdb=" CG GLN C 316 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.11e+00 angle pdb=" N GLU C 312 " pdb=" CA GLU C 312 " pdb=" C GLU C 312 " ideal model delta sigma weight residual 113.18 110.00 3.18 1.33e+00 5.65e-01 5.72e+00 angle pdb=" C ALA C 272 " pdb=" N CYS C 273 " pdb=" CA CYS C 273 " ideal model delta sigma weight residual 125.02 120.94 4.08 1.76e+00 3.23e-01 5.37e+00 ... (remaining 25171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 10446 17.76 - 35.52: 760 35.52 - 53.28: 141 53.28 - 71.04: 27 71.04 - 88.80: 20 Dihedral angle restraints: 11394 sinusoidal: 4194 harmonic: 7200 Sorted by residual: dihedral pdb=" CA HIS D 435 " pdb=" C HIS D 435 " pdb=" N ILE D 436 " pdb=" CA ILE D 436 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA HIS C 435 " pdb=" C HIS C 435 " pdb=" N ILE C 436 " pdb=" CA ILE C 436 " ideal model delta harmonic sigma weight residual 180.00 160.37 19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA HIS F 435 " pdb=" C HIS F 435 " pdb=" N ILE F 436 " pdb=" CA ILE F 436 " ideal model delta harmonic sigma weight residual 180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 11391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1981 0.032 - 0.063: 573 0.063 - 0.095: 219 0.095 - 0.126: 200 0.126 - 0.158: 21 Chirality restraints: 2994 Sorted by residual: chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.21e-01 chirality pdb=" CA ILE D 240 " pdb=" N ILE D 240 " pdb=" C ILE D 240 " pdb=" CB ILE D 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ILE F 354 " pdb=" N ILE F 354 " pdb=" C ILE F 354 " pdb=" CB ILE F 354 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2991 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 206 " 0.151 9.50e-02 1.11e+02 6.81e-02 3.42e+00 pdb=" NE ARG A 206 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 206 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 206 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 206 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 364 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C PHE E 364 " 0.031 2.00e-02 2.50e+03 pdb=" O PHE E 364 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP E 365 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 349 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO C 350 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 350 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 350 " 0.019 5.00e-02 4.00e+02 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 228 2.59 - 3.16: 17077 3.16 - 3.74: 28469 3.74 - 4.32: 37569 4.32 - 4.90: 64115 Nonbonded interactions: 147458 Sorted by model distance: nonbonded pdb=" OD1 ASN B 371 " pdb=" OG SER B 416 " model vdw 2.008 3.040 nonbonded pdb=" OD1 ASN E 371 " pdb=" OG SER E 416 " model vdw 2.058 3.040 nonbonded pdb=" OG SER D 472 " pdb=" O ALA D 500 " model vdw 2.060 3.040 nonbonded pdb=" O ASP F 451 " pdb=" OG1 THR F 473 " model vdw 2.074 3.040 nonbonded pdb=" N GLN B 316 " pdb=" OE1 GLN B 316 " model vdw 2.094 3.120 ... (remaining 147453 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.510 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18552 Z= 0.132 Angle : 0.496 9.637 25176 Z= 0.271 Chirality : 0.044 0.158 2994 Planarity : 0.003 0.068 3360 Dihedral : 13.401 88.801 6750 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.06 % Allowed : 10.02 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.18), residues: 2520 helix: 1.78 (0.17), residues: 1072 sheet: -0.48 (0.24), residues: 488 loop : 0.16 (0.22), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 206 TYR 0.016 0.001 TYR C 486 PHE 0.008 0.001 PHE E 480 TRP 0.008 0.001 TRP C 481 HIS 0.003 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00271 (18552) covalent geometry : angle 0.49590 (25176) hydrogen bonds : bond 0.14385 ( 942) hydrogen bonds : angle 6.13999 ( 2748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 737 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8167 (m-80) cc_final: 0.7870 (m-10) REVERT: A 256 PHE cc_start: 0.9085 (m-10) cc_final: 0.8755 (m-10) REVERT: A 287 LYS cc_start: 0.8276 (pttm) cc_final: 0.7957 (pttt) REVERT: A 339 ARG cc_start: 0.8314 (mtp85) cc_final: 0.7870 (tpp80) REVERT: A 346 LEU cc_start: 0.8896 (mt) cc_final: 0.7953 (mt) REVERT: A 391 SER cc_start: 0.8887 (t) cc_final: 0.8578 (m) REVERT: B 294 MET cc_start: 0.8642 (mmm) cc_final: 0.8004 (mmm) REVERT: B 313 LEU cc_start: 0.8215 (mp) cc_final: 0.7887 (mp) REVERT: B 342 VAL cc_start: 0.7531 (t) cc_final: 0.7183 (t) REVERT: B 346 LEU cc_start: 0.8475 (mt) cc_final: 0.8235 (mt) REVERT: B 365 ASP cc_start: 0.7907 (m-30) cc_final: 0.7682 (m-30) REVERT: B 448 VAL cc_start: 0.8866 (t) cc_final: 0.8546 (p) REVERT: C 239 THR cc_start: 0.7773 (m) cc_final: 0.7288 (p) REVERT: C 270 ILE cc_start: 0.8118 (mt) cc_final: 0.7690 (mm) REVERT: C 317 GLN cc_start: 0.8715 (mm-40) cc_final: 0.7371 (mm-40) REVERT: C 358 VAL cc_start: 0.8447 (t) cc_final: 0.8053 (m) REVERT: C 367 LEU cc_start: 0.8446 (mp) cc_final: 0.7814 (mp) REVERT: C 381 LEU cc_start: 0.7720 (tp) cc_final: 0.7420 (tp) REVERT: C 410 LYS cc_start: 0.7747 (mttm) cc_final: 0.7040 (mtmm) REVERT: C 411 GLU cc_start: 0.8855 (tp30) cc_final: 0.8615 (tp30) REVERT: D 207 VAL cc_start: 0.7304 (p) cc_final: 0.6519 (p) REVERT: D 240 ILE cc_start: 0.7152 (mm) cc_final: 0.6751 (mm) REVERT: D 247 LYS cc_start: 0.8730 (mptt) cc_final: 0.8433 (mmtt) REVERT: D 410 LYS cc_start: 0.8606 (mttm) cc_final: 0.8270 (mttm) REVERT: D 454 VAL cc_start: 0.8216 (t) cc_final: 0.7932 (p) REVERT: E 175 VAL cc_start: 0.8384 (p) cc_final: 0.8041 (m) REVERT: E 243 PHE cc_start: 0.7955 (t80) cc_final: 0.6867 (t80) REVERT: E 294 MET cc_start: 0.7002 (mmm) cc_final: 0.6179 (mmm) REVERT: E 312 GLU cc_start: 0.8321 (tp30) cc_final: 0.8022 (tp30) REVERT: E 325 THR cc_start: 0.8250 (p) cc_final: 0.7810 (p) REVERT: E 395 SER cc_start: 0.9272 (m) cc_final: 0.8989 (p) REVERT: F 289 THR cc_start: 0.9118 (m) cc_final: 0.8824 (t) REVERT: F 290 LEU cc_start: 0.9352 (tp) cc_final: 0.9145 (tt) REVERT: F 380 THR cc_start: 0.7409 (p) cc_final: 0.6981 (p) REVERT: F 437 THR cc_start: 0.7100 (p) cc_final: 0.6763 (t) REVERT: F 489 LEU cc_start: 0.8806 (mm) cc_final: 0.8411 (mp) outliers start: 1 outliers final: 0 residues processed: 737 average time/residue: 0.1504 time to fit residues: 157.8211 Evaluate side-chains 504 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 30.0000 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 40.0000 chunk 247 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 10.0000 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 ASN B 169 HIS ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 ASN B 382 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN D 374 HIS E 371 ASN F 382 HIS ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.086491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.064989 restraints weight = 55647.480| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 4.71 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18552 Z= 0.193 Angle : 0.712 9.282 25176 Z= 0.372 Chirality : 0.050 0.218 2994 Planarity : 0.006 0.077 3360 Dihedral : 4.280 32.395 2754 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.55 % Allowed : 19.09 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 2520 helix: 1.50 (0.16), residues: 1100 sheet: -0.63 (0.21), residues: 588 loop : 0.56 (0.24), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 352 TYR 0.016 0.002 TYR D 402 PHE 0.027 0.002 PHE A 243 TRP 0.016 0.003 TRP C 481 HIS 0.006 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00441 (18552) covalent geometry : angle 0.71216 (25176) hydrogen bonds : bond 0.04548 ( 942) hydrogen bonds : angle 4.88341 ( 2748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 528 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8505 (m-80) cc_final: 0.8183 (m-10) REVERT: A 243 PHE cc_start: 0.8090 (p90) cc_final: 0.7691 (p90) REVERT: A 256 PHE cc_start: 0.9259 (m-10) cc_final: 0.8908 (m-10) REVERT: A 314 GLN cc_start: 0.8362 (tp40) cc_final: 0.8146 (tp40) REVERT: A 339 ARG cc_start: 0.8274 (mtp85) cc_final: 0.7943 (ttm-80) REVERT: A 342 VAL cc_start: 0.9004 (t) cc_final: 0.8717 (t) REVERT: A 345 CYS cc_start: 0.8117 (m) cc_final: 0.7816 (m) REVERT: A 391 SER cc_start: 0.8794 (t) cc_final: 0.8432 (m) REVERT: A 408 THR cc_start: 0.7978 (p) cc_final: 0.7712 (p) REVERT: A 411 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8725 (tm-30) REVERT: A 456 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8451 (pm20) REVERT: B 151 LEU cc_start: 0.9356 (mt) cc_final: 0.9152 (mt) REVERT: B 162 ASP cc_start: 0.7477 (m-30) cc_final: 0.6995 (t0) REVERT: B 164 MET cc_start: 0.7725 (mtm) cc_final: 0.7349 (mpp) REVERT: B 239 THR cc_start: 0.8518 (m) cc_final: 0.8295 (p) REVERT: B 277 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6129 (mt) REVERT: B 313 LEU cc_start: 0.8550 (mp) cc_final: 0.8339 (mp) REVERT: B 314 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 342 VAL cc_start: 0.7682 (t) cc_final: 0.7405 (t) REVERT: B 343 LYS cc_start: 0.8663 (mttp) cc_final: 0.8343 (mttm) REVERT: B 364 PHE cc_start: 0.8957 (t80) cc_final: 0.8606 (t80) REVERT: B 365 ASP cc_start: 0.8440 (m-30) cc_final: 0.8018 (m-30) REVERT: B 410 LYS cc_start: 0.8550 (mtpt) cc_final: 0.8079 (mtpt) REVERT: B 438 GLU cc_start: 0.7714 (mp0) cc_final: 0.7489 (mp0) REVERT: B 465 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8445 (mtmt) REVERT: C 244 LYS cc_start: 0.9305 (mmmt) cc_final: 0.8399 (tptt) REVERT: C 317 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8443 (mm-40) REVERT: C 339 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8361 (mtp85) REVERT: C 343 LYS cc_start: 0.8729 (mttp) cc_final: 0.8421 (mttp) REVERT: C 345 CYS cc_start: 0.8018 (m) cc_final: 0.7584 (m) REVERT: C 358 VAL cc_start: 0.8593 (t) cc_final: 0.8297 (t) REVERT: C 364 PHE cc_start: 0.8407 (t80) cc_final: 0.7810 (t80) REVERT: C 368 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7850 (mm110) REVERT: C 399 MET cc_start: 0.9200 (ptp) cc_final: 0.8994 (ptp) REVERT: C 411 GLU cc_start: 0.8946 (tp30) cc_final: 0.8591 (tp30) REVERT: C 450 GLN cc_start: 0.7978 (pp30) cc_final: 0.7775 (pp30) REVERT: C 469 LYS cc_start: 0.9390 (mmmt) cc_final: 0.8762 (mmmt) REVERT: D 205 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8304 (mtp85) REVERT: D 368 GLN cc_start: 0.9007 (mt0) cc_final: 0.8806 (mt0) REVERT: D 378 MET cc_start: 0.7412 (mtp) cc_final: 0.7161 (mtp) REVERT: D 390 ILE cc_start: 0.9057 (mt) cc_final: 0.8815 (mt) REVERT: D 407 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8039 (mmmm) REVERT: D 411 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8766 (mt-10) REVERT: D 491 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7940 (ttp80) REVERT: D 495 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8814 (mt-10) REVERT: E 180 GLN cc_start: 0.7637 (pp30) cc_final: 0.7410 (pp30) REVERT: E 243 PHE cc_start: 0.7786 (t80) cc_final: 0.6698 (t80) REVERT: E 256 PHE cc_start: 0.8495 (m-10) cc_final: 0.8251 (m-10) REVERT: E 341 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7202 (mm) REVERT: E 345 CYS cc_start: 0.8800 (m) cc_final: 0.8463 (m) REVERT: E 359 ARG cc_start: 0.8312 (ttp80) cc_final: 0.8041 (ttp80) REVERT: E 410 LYS cc_start: 0.8539 (mttm) cc_final: 0.7973 (mtpt) REVERT: E 481 TRP cc_start: 0.8696 (t-100) cc_final: 0.8393 (t-100) REVERT: F 178 LYS cc_start: 0.9253 (ttpp) cc_final: 0.8988 (tmmt) REVERT: F 202 GLN cc_start: 0.7858 (mp10) cc_final: 0.7505 (mp10) REVERT: F 256 PHE cc_start: 0.9087 (m-10) cc_final: 0.8813 (m-10) REVERT: F 289 THR cc_start: 0.9322 (m) cc_final: 0.8989 (t) REVERT: F 324 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6742 (tp30) REVERT: F 342 VAL cc_start: 0.9406 (t) cc_final: 0.9151 (p) REVERT: F 345 CYS cc_start: 0.8622 (m) cc_final: 0.8129 (m) REVERT: F 378 MET cc_start: 0.8053 (mpp) cc_final: 0.7822 (mpp) REVERT: F 396 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8061 (ttm) REVERT: F 399 MET cc_start: 0.9314 (ptm) cc_final: 0.9114 (ppp) REVERT: F 407 LYS cc_start: 0.8834 (tppt) cc_final: 0.8535 (tppt) REVERT: F 409 ILE cc_start: 0.7998 (mt) cc_final: 0.7658 (mt) REVERT: F 410 LYS cc_start: 0.8241 (mttm) cc_final: 0.7915 (mtmt) REVERT: F 411 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8650 (pp20) outliers start: 63 outliers final: 34 residues processed: 554 average time/residue: 0.1347 time to fit residues: 110.1414 Evaluate side-chains 476 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 437 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 364 PHE Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 491 ARG Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain F residue 196 CYS Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 36 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 206 optimal weight: 50.0000 chunk 177 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 107 optimal weight: 40.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 ASN A 316 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 HIS C 344 ASN D 191 GLN D 225 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 HIS F 422 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.066619 restraints weight = 55191.082| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 4.52 r_work: 0.2913 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18552 Z= 0.169 Angle : 0.669 11.038 25176 Z= 0.343 Chirality : 0.048 0.203 2994 Planarity : 0.005 0.060 3360 Dihedral : 4.181 31.920 2754 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.56 % Allowed : 20.21 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.17), residues: 2520 helix: 1.57 (0.16), residues: 1100 sheet: -0.62 (0.21), residues: 566 loop : 0.36 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 206 TYR 0.015 0.001 TYR D 402 PHE 0.023 0.002 PHE A 243 TRP 0.012 0.002 TRP E 481 HIS 0.004 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00391 (18552) covalent geometry : angle 0.66894 (25176) hydrogen bonds : bond 0.03745 ( 942) hydrogen bonds : angle 4.58025 ( 2748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 470 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8570 (m-80) cc_final: 0.8276 (m-10) REVERT: A 243 PHE cc_start: 0.8250 (p90) cc_final: 0.7801 (p90) REVERT: A 256 PHE cc_start: 0.9268 (m-10) cc_final: 0.9000 (m-10) REVERT: A 314 GLN cc_start: 0.8870 (tp40) cc_final: 0.8241 (tm-30) REVERT: A 391 SER cc_start: 0.9053 (t) cc_final: 0.8734 (m) REVERT: B 164 MET cc_start: 0.8432 (mtm) cc_final: 0.8087 (mpp) REVERT: B 184 VAL cc_start: 0.8152 (t) cc_final: 0.7747 (p) REVERT: B 239 THR cc_start: 0.8842 (m) cc_final: 0.8634 (p) REVERT: B 273 CYS cc_start: 0.9066 (m) cc_final: 0.8434 (p) REVERT: B 313 LEU cc_start: 0.8870 (mp) cc_final: 0.8473 (mp) REVERT: B 314 GLN cc_start: 0.8901 (tm-30) cc_final: 0.8554 (tm-30) REVERT: B 339 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8924 (ttm-80) REVERT: B 450 GLN cc_start: 0.9288 (pt0) cc_final: 0.9025 (pt0) REVERT: C 243 PHE cc_start: 0.8078 (t80) cc_final: 0.7376 (t80) REVERT: C 244 LYS cc_start: 0.9334 (mmmt) cc_final: 0.8348 (tptt) REVERT: C 250 MET cc_start: 0.8215 (ttt) cc_final: 0.7828 (pmm) REVERT: C 270 ILE cc_start: 0.9229 (mt) cc_final: 0.8868 (mm) REVERT: C 317 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8337 (mm-40) REVERT: C 343 LYS cc_start: 0.9007 (mttp) cc_final: 0.8689 (mttp) REVERT: C 364 PHE cc_start: 0.8683 (t80) cc_final: 0.7916 (t80) REVERT: C 368 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8065 (mm110) REVERT: C 370 MET cc_start: 0.8547 (mmt) cc_final: 0.8343 (mmt) REVERT: C 412 MET cc_start: 0.9366 (ttp) cc_final: 0.9159 (ttt) REVERT: C 450 GLN cc_start: 0.8419 (pp30) cc_final: 0.7750 (pp30) REVERT: C 453 PHE cc_start: 0.6250 (OUTLIER) cc_final: 0.5872 (t80) REVERT: C 456 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: C 469 LYS cc_start: 0.9071 (mmmt) cc_final: 0.8810 (tptp) REVERT: C 482 ASP cc_start: 0.9404 (OUTLIER) cc_final: 0.9183 (p0) REVERT: D 205 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8386 (mtp85) REVERT: D 233 LEU cc_start: 0.9288 (mm) cc_final: 0.9035 (mm) REVERT: D 243 PHE cc_start: 0.7268 (m-10) cc_final: 0.7001 (m-80) REVERT: D 251 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9223 (mmmt) REVERT: D 343 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8533 (mttm) REVERT: D 378 MET cc_start: 0.8183 (mtp) cc_final: 0.7940 (mtp) REVERT: D 390 ILE cc_start: 0.9192 (mt) cc_final: 0.8990 (mt) REVERT: D 407 LYS cc_start: 0.8807 (mtpp) cc_final: 0.8339 (mmmm) REVERT: D 426 LEU cc_start: 0.8847 (mt) cc_final: 0.8607 (mt) REVERT: D 448 VAL cc_start: 0.9163 (t) cc_final: 0.8856 (p) REVERT: D 491 ARG cc_start: 0.8912 (ttp80) cc_final: 0.8448 (ttp80) REVERT: E 180 GLN cc_start: 0.8376 (pp30) cc_final: 0.8013 (pp30) REVERT: E 256 PHE cc_start: 0.8541 (m-10) cc_final: 0.8316 (m-10) REVERT: E 312 GLU cc_start: 0.8477 (tp30) cc_final: 0.8193 (mp0) REVERT: E 339 ARG cc_start: 0.8840 (ttm110) cc_final: 0.8574 (ttm-80) REVERT: E 345 CYS cc_start: 0.9305 (m) cc_final: 0.9074 (m) REVERT: E 388 GLU cc_start: 0.9450 (tp30) cc_final: 0.9088 (tt0) REVERT: E 418 ASP cc_start: 0.8264 (m-30) cc_final: 0.7848 (m-30) REVERT: E 481 TRP cc_start: 0.8832 (t-100) cc_final: 0.8430 (t-100) REVERT: F 148 TYR cc_start: 0.8821 (m-80) cc_final: 0.8106 (m-10) REVERT: F 178 LYS cc_start: 0.9428 (ttpp) cc_final: 0.9184 (ttpp) REVERT: F 180 GLN cc_start: 0.8873 (pm20) cc_final: 0.8460 (pm20) REVERT: F 193 MET cc_start: 0.9318 (tpp) cc_final: 0.9091 (tpp) REVERT: F 202 GLN cc_start: 0.8591 (mp10) cc_final: 0.8030 (mp10) REVERT: F 256 PHE cc_start: 0.9210 (m-10) cc_final: 0.8882 (m-10) REVERT: F 289 THR cc_start: 0.9508 (m) cc_final: 0.9187 (t) REVERT: F 297 PHE cc_start: 0.9328 (m-80) cc_final: 0.8918 (m-80) REVERT: F 324 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7605 (tp30) REVERT: F 378 MET cc_start: 0.9019 (mpp) cc_final: 0.8687 (mpt) REVERT: F 396 MET cc_start: 0.8684 (ttm) cc_final: 0.8409 (ttm) REVERT: F 399 MET cc_start: 0.9404 (ptm) cc_final: 0.9121 (ppp) REVERT: F 407 LYS cc_start: 0.9033 (tppt) cc_final: 0.8812 (tppt) REVERT: F 410 LYS cc_start: 0.8399 (mttm) cc_final: 0.8195 (mtmt) outliers start: 81 outliers final: 43 residues processed: 512 average time/residue: 0.1282 time to fit residues: 98.4496 Evaluate side-chains 466 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 420 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 99 optimal weight: 9.9990 chunk 129 optimal weight: 9.9990 chunk 240 optimal weight: 30.0000 chunk 193 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 121 optimal weight: 30.0000 chunk 78 optimal weight: 5.9990 chunk 199 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 178 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN D 191 GLN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 374 HIS E 344 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.085790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.064221 restraints weight = 55824.333| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 4.72 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18552 Z= 0.185 Angle : 0.661 11.293 25176 Z= 0.339 Chirality : 0.048 0.216 2994 Planarity : 0.005 0.047 3360 Dihedral : 4.159 32.269 2754 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.90 % Allowed : 20.95 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.17), residues: 2520 helix: 1.50 (0.16), residues: 1102 sheet: -0.59 (0.21), residues: 562 loop : 0.19 (0.23), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 206 TYR 0.013 0.001 TYR D 402 PHE 0.017 0.002 PHE A 243 TRP 0.012 0.002 TRP B 481 HIS 0.003 0.001 HIS D 382 Details of bonding type rmsd covalent geometry : bond 0.00410 (18552) covalent geometry : angle 0.66059 (25176) hydrogen bonds : bond 0.03613 ( 942) hydrogen bonds : angle 4.53478 ( 2748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 438 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.8843 (m-80) cc_final: 0.8490 (m-10) REVERT: A 243 PHE cc_start: 0.8365 (p90) cc_final: 0.7922 (p90) REVERT: A 256 PHE cc_start: 0.9280 (m-10) cc_final: 0.9030 (m-10) REVERT: A 314 GLN cc_start: 0.8772 (tp40) cc_final: 0.8257 (tm-30) REVERT: A 316 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8567 (tm-30) REVERT: A 324 GLU cc_start: 0.8524 (pp20) cc_final: 0.8255 (pp20) REVERT: A 368 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8670 (tm-30) REVERT: A 391 SER cc_start: 0.9149 (t) cc_final: 0.8836 (m) REVERT: B 180 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8859 (tm-30) REVERT: B 313 LEU cc_start: 0.9082 (mp) cc_final: 0.8760 (mp) REVERT: B 314 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7998 (tm-30) REVERT: B 338 MET cc_start: 0.8926 (mmt) cc_final: 0.8680 (tpp) REVERT: B 346 LEU cc_start: 0.8901 (mt) cc_final: 0.8664 (mm) REVERT: B 355 VAL cc_start: 0.9340 (t) cc_final: 0.9124 (t) REVERT: B 364 PHE cc_start: 0.9167 (t80) cc_final: 0.8754 (t80) REVERT: B 368 GLN cc_start: 0.8269 (mt0) cc_final: 0.7555 (mt0) REVERT: B 450 GLN cc_start: 0.9227 (pt0) cc_final: 0.9008 (pt0) REVERT: C 180 GLN cc_start: 0.8429 (pp30) cc_final: 0.7975 (tm-30) REVERT: C 243 PHE cc_start: 0.8256 (t80) cc_final: 0.7669 (t80) REVERT: C 244 LYS cc_start: 0.9331 (mmmt) cc_final: 0.8647 (tptp) REVERT: C 270 ILE cc_start: 0.9412 (mt) cc_final: 0.9187 (mm) REVERT: C 343 LYS cc_start: 0.9076 (mttp) cc_final: 0.8548 (mmtm) REVERT: C 364 PHE cc_start: 0.8786 (t80) cc_final: 0.8075 (t80) REVERT: C 368 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8021 (mm110) REVERT: C 412 MET cc_start: 0.9464 (ttp) cc_final: 0.9249 (ttt) REVERT: C 450 GLN cc_start: 0.7577 (pp30) cc_final: 0.7299 (pp30) REVERT: C 453 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.6152 (t80) REVERT: C 475 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8228 (pt) REVERT: C 482 ASP cc_start: 0.9322 (OUTLIER) cc_final: 0.9072 (p0) REVERT: D 193 MET cc_start: 0.8251 (tpt) cc_final: 0.7946 (tpt) REVERT: D 202 GLN cc_start: 0.8762 (tt0) cc_final: 0.8436 (mm110) REVERT: D 233 LEU cc_start: 0.9364 (mm) cc_final: 0.9104 (mm) REVERT: D 308 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.5733 (pt0) REVERT: D 339 ARG cc_start: 0.8609 (ptm160) cc_final: 0.8108 (ptm160) REVERT: D 343 LYS cc_start: 0.9066 (mtpt) cc_final: 0.8578 (mttm) REVERT: D 426 LEU cc_start: 0.8868 (mt) cc_final: 0.8601 (mt) REVERT: E 180 GLN cc_start: 0.8210 (pp30) cc_final: 0.7858 (pp30) REVERT: E 243 PHE cc_start: 0.7954 (t80) cc_final: 0.7680 (t80) REVERT: E 256 PHE cc_start: 0.8756 (m-10) cc_final: 0.8488 (m-10) REVERT: E 312 GLU cc_start: 0.8408 (tp30) cc_final: 0.8071 (mp0) REVERT: E 345 CYS cc_start: 0.9261 (m) cc_final: 0.8810 (m) REVERT: E 388 GLU cc_start: 0.9309 (tp30) cc_final: 0.9006 (tp30) REVERT: E 418 ASP cc_start: 0.8280 (m-30) cc_final: 0.7901 (m-30) REVERT: E 469 LYS cc_start: 0.9485 (ttpp) cc_final: 0.9280 (tmmt) REVERT: E 481 TRP cc_start: 0.8853 (t-100) cc_final: 0.8587 (t-100) REVERT: F 148 TYR cc_start: 0.8744 (m-80) cc_final: 0.8487 (m-10) REVERT: F 178 LYS cc_start: 0.9427 (ttpp) cc_final: 0.9088 (tmmt) REVERT: F 180 GLN cc_start: 0.8627 (pm20) cc_final: 0.7973 (pm20) REVERT: F 202 GLN cc_start: 0.8702 (mp10) cc_final: 0.7995 (mp10) REVERT: F 256 PHE cc_start: 0.9327 (m-10) cc_final: 0.8957 (m-10) REVERT: F 297 PHE cc_start: 0.9270 (m-80) cc_final: 0.8969 (m-10) REVERT: F 324 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7191 (tp30) REVERT: F 349 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.8121 (ttt-90) REVERT: F 357 GLU cc_start: 0.8129 (tt0) cc_final: 0.7630 (tm-30) REVERT: F 396 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8526 (ttm) REVERT: F 399 MET cc_start: 0.9369 (ptm) cc_final: 0.9027 (ppp) REVERT: F 407 LYS cc_start: 0.8992 (tppt) cc_final: 0.8738 (tppt) REVERT: F 410 LYS cc_start: 0.8320 (mttm) cc_final: 0.8069 (mtpt) outliers start: 87 outliers final: 52 residues processed: 485 average time/residue: 0.1312 time to fit residues: 95.3921 Evaluate side-chains 449 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 390 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 316 GLN Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 487 TYR Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 453 PHE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 482 ASP Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 365 ASP Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 407 LYS Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 345 CYS Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 88 optimal weight: 50.0000 chunk 163 optimal weight: 8.9990 chunk 81 optimal weight: 40.0000 chunk 47 optimal weight: 30.0000 chunk 84 optimal weight: 120.0000 chunk 49 optimal weight: 8.9990 chunk 46 optimal weight: 50.0000 chunk 82 optimal weight: 20.0000 chunk 32 optimal weight: 0.5980 chunk 85 optimal weight: 30.0000 chunk 101 optimal weight: 20.0000 overall best weight: 11.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN B 169 HIS B 276 ASN C 344 ASN D 191 GLN D 225 ASN ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.083246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062245 restraints weight = 55700.615| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 4.65 r_work: 0.2787 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.7853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.165 18552 Z= 0.296 Angle : 0.783 10.346 25176 Z= 0.401 Chirality : 0.051 0.354 2994 Planarity : 0.006 0.064 3360 Dihedral : 4.521 34.065 2754 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.19 % Allowed : 21.00 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.17), residues: 2520 helix: 1.24 (0.16), residues: 1102 sheet: -0.73 (0.21), residues: 564 loop : 0.01 (0.23), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 339 TYR 0.021 0.002 TYR D 402 PHE 0.034 0.002 PHE D 256 TRP 0.013 0.002 TRP B 481 HIS 0.008 0.001 HIS D 382 Details of bonding type rmsd covalent geometry : bond 0.00682 (18552) covalent geometry : angle 0.78310 (25176) hydrogen bonds : bond 0.04095 ( 942) hydrogen bonds : angle 4.82614 ( 2748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 350 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9161 (m-80) cc_final: 0.8575 (m-10) REVERT: A 243 PHE cc_start: 0.8708 (p90) cc_final: 0.8197 (p90) REVERT: A 314 GLN cc_start: 0.8912 (tp40) cc_final: 0.8364 (tm-30) REVERT: A 316 GLN cc_start: 0.8915 (mm110) cc_final: 0.8580 (mp10) REVERT: A 324 GLU cc_start: 0.8964 (pp20) cc_final: 0.8554 (pp20) REVERT: A 368 GLN cc_start: 0.9333 (tm-30) cc_final: 0.8858 (tm-30) REVERT: A 372 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8905 (p) REVERT: A 391 SER cc_start: 0.9422 (t) cc_final: 0.9036 (p) REVERT: B 180 GLN cc_start: 0.9362 (tm-30) cc_final: 0.8886 (tm-30) REVERT: B 190 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9216 (tp) REVERT: B 242 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8994 (mttt) REVERT: B 256 PHE cc_start: 0.9035 (m-10) cc_final: 0.8779 (m-10) REVERT: B 339 ARG cc_start: 0.9396 (ttp80) cc_final: 0.8684 (mmm-85) REVERT: B 343 LYS cc_start: 0.9389 (mttp) cc_final: 0.9083 (mttm) REVERT: B 364 PHE cc_start: 0.9386 (t80) cc_final: 0.9172 (t80) REVERT: B 368 GLN cc_start: 0.8770 (mt0) cc_final: 0.8459 (mt0) REVERT: C 148 TYR cc_start: 0.8807 (m-10) cc_final: 0.8507 (m-10) REVERT: C 206 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8205 (ttp80) REVERT: C 309 ASP cc_start: 0.8512 (p0) cc_final: 0.8230 (p0) REVERT: C 312 GLU cc_start: 0.8933 (tp30) cc_final: 0.8630 (tm-30) REVERT: C 347 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8809 (ttm110) REVERT: C 364 PHE cc_start: 0.9195 (t80) cc_final: 0.8786 (t80) REVERT: C 368 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8704 (mm-40) REVERT: D 194 ASN cc_start: 0.9360 (m-40) cc_final: 0.9123 (m110) REVERT: D 202 GLN cc_start: 0.9037 (tt0) cc_final: 0.8650 (tm-30) REVERT: D 215 ASP cc_start: 0.8590 (t0) cc_final: 0.7937 (m-30) REVERT: D 217 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7875 (tpt-90) REVERT: D 233 LEU cc_start: 0.9447 (mm) cc_final: 0.9231 (mm) REVERT: D 243 PHE cc_start: 0.7154 (m-10) cc_final: 0.5970 (m-10) REVERT: D 278 VAL cc_start: 0.8656 (t) cc_final: 0.8421 (p) REVERT: D 343 LYS cc_start: 0.9293 (mtpt) cc_final: 0.8788 (mttm) REVERT: D 465 LYS cc_start: 0.9277 (tmtt) cc_final: 0.9070 (tmtt) REVERT: E 180 GLN cc_start: 0.8766 (pp30) cc_final: 0.8338 (pp30) REVERT: E 211 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8666 (p) REVERT: E 256 PHE cc_start: 0.9049 (m-10) cc_final: 0.8773 (m-10) REVERT: E 312 GLU cc_start: 0.8833 (tp30) cc_final: 0.8486 (mp0) REVERT: E 339 ARG cc_start: 0.9470 (ttp80) cc_final: 0.9247 (ttp80) REVERT: E 359 ARG cc_start: 0.9309 (ttp80) cc_final: 0.9067 (ttp80) REVERT: E 406 SER cc_start: 0.9120 (m) cc_final: 0.8824 (t) REVERT: E 418 ASP cc_start: 0.8597 (m-30) cc_final: 0.7914 (m-30) REVERT: F 148 TYR cc_start: 0.9062 (m-80) cc_final: 0.8815 (m-80) REVERT: F 178 LYS cc_start: 0.9585 (ttpp) cc_final: 0.9297 (ttpp) REVERT: F 180 GLN cc_start: 0.9021 (pm20) cc_final: 0.8307 (pm20) REVERT: F 191 GLN cc_start: 0.9037 (tt0) cc_final: 0.8787 (tt0) REVERT: F 202 GLN cc_start: 0.9283 (mp10) cc_final: 0.8498 (mp10) REVERT: F 256 PHE cc_start: 0.9455 (m-10) cc_final: 0.9003 (m-10) REVERT: F 312 GLU cc_start: 0.8466 (pm20) cc_final: 0.8220 (pm20) REVERT: F 314 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7852 (tm-30) REVERT: F 340 ASP cc_start: 0.9687 (t0) cc_final: 0.9451 (m-30) REVERT: F 345 CYS cc_start: 0.9358 (m) cc_final: 0.9024 (t) REVERT: F 349 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8804 (tpt-90) REVERT: F 353 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8087 (tt) REVERT: F 402 TYR cc_start: 0.8310 (m-80) cc_final: 0.8089 (m-80) REVERT: F 407 LYS cc_start: 0.9196 (tppt) cc_final: 0.8933 (tppt) outliers start: 110 outliers final: 63 residues processed: 425 average time/residue: 0.1317 time to fit residues: 84.2428 Evaluate side-chains 382 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 463 HIS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 211 SER Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 353 ILE Chi-restraints excluded: chain F residue 366 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 215 optimal weight: 50.0000 chunk 56 optimal weight: 6.9990 chunk 129 optimal weight: 40.0000 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 162 optimal weight: 0.0980 chunk 174 optimal weight: 30.0000 chunk 42 optimal weight: 110.0000 chunk 18 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 84 optimal weight: 120.0000 overall best weight: 6.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 276 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 ASN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.084398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.063086 restraints weight = 54365.847| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.58 r_work: 0.2819 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.8205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18552 Z= 0.171 Angle : 0.673 10.771 25176 Z= 0.335 Chirality : 0.049 0.311 2994 Planarity : 0.005 0.049 3360 Dihedral : 4.338 34.575 2754 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.34 % Allowed : 23.09 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.17), residues: 2520 helix: 1.42 (0.16), residues: 1102 sheet: -0.74 (0.21), residues: 560 loop : 0.13 (0.23), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 491 TYR 0.017 0.001 TYR D 402 PHE 0.018 0.002 PHE F 364 TRP 0.014 0.002 TRP E 481 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00405 (18552) covalent geometry : angle 0.67332 (25176) hydrogen bonds : bond 0.03497 ( 942) hydrogen bonds : angle 4.58447 ( 2748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 344 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9171 (m-80) cc_final: 0.8823 (m-10) REVERT: A 202 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 243 PHE cc_start: 0.8748 (p90) cc_final: 0.8281 (p90) REVERT: A 314 GLN cc_start: 0.8908 (tp40) cc_final: 0.8350 (tm-30) REVERT: A 324 GLU cc_start: 0.8870 (pp20) cc_final: 0.8438 (pp20) REVERT: A 347 ARG cc_start: 0.9526 (OUTLIER) cc_final: 0.9249 (ttp-110) REVERT: A 368 GLN cc_start: 0.9356 (tm-30) cc_final: 0.8865 (tm-30) REVERT: A 391 SER cc_start: 0.9392 (t) cc_final: 0.9007 (p) REVERT: B 180 GLN cc_start: 0.9376 (tm-30) cc_final: 0.8970 (tm-30) REVERT: B 190 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9194 (tp) REVERT: B 202 GLN cc_start: 0.9416 (tt0) cc_final: 0.9074 (tm-30) REVERT: B 256 PHE cc_start: 0.9057 (m-10) cc_final: 0.8801 (m-10) REVERT: B 343 LYS cc_start: 0.9388 (mttp) cc_final: 0.9151 (mttp) REVERT: B 364 PHE cc_start: 0.9412 (t80) cc_final: 0.9074 (t80) REVERT: B 368 GLN cc_start: 0.8740 (mt0) cc_final: 0.8340 (mt0) REVERT: B 418 ASP cc_start: 0.8282 (m-30) cc_final: 0.7763 (m-30) REVERT: C 148 TYR cc_start: 0.8802 (m-10) cc_final: 0.8368 (m-10) REVERT: C 158 ASP cc_start: 0.9090 (p0) cc_final: 0.8890 (p0) REVERT: C 180 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8689 (pp30) REVERT: C 244 LYS cc_start: 0.9609 (mmmt) cc_final: 0.9130 (tptp) REVERT: C 312 GLU cc_start: 0.9000 (tp30) cc_final: 0.8765 (tm-30) REVERT: C 339 ARG cc_start: 0.9277 (ttm-80) cc_final: 0.8824 (ttm-80) REVERT: C 364 PHE cc_start: 0.9076 (t80) cc_final: 0.8846 (t80) REVERT: C 411 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8693 (mp0) REVERT: C 482 ASP cc_start: 0.9577 (p0) cc_final: 0.9367 (p0) REVERT: D 202 GLN cc_start: 0.9073 (tt0) cc_final: 0.8696 (tm-30) REVERT: D 215 ASP cc_start: 0.8521 (t0) cc_final: 0.8233 (m-30) REVERT: D 343 LYS cc_start: 0.9328 (mtpt) cc_final: 0.8831 (mttm) REVERT: D 359 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8673 (ttm110) REVERT: D 364 PHE cc_start: 0.8906 (t80) cc_final: 0.8576 (t80) REVERT: D 438 GLU cc_start: 0.8174 (pt0) cc_final: 0.7959 (pt0) REVERT: E 180 GLN cc_start: 0.8861 (pp30) cc_final: 0.8435 (pp30) REVERT: E 275 CYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8288 (m) REVERT: E 359 ARG cc_start: 0.9180 (ttp80) cc_final: 0.8798 (ttp80) REVERT: E 388 GLU cc_start: 0.9466 (tp30) cc_final: 0.9123 (tp30) REVERT: E 394 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9013 (tm-30) REVERT: E 406 SER cc_start: 0.9092 (m) cc_final: 0.8847 (t) REVERT: E 418 ASP cc_start: 0.8678 (m-30) cc_final: 0.8226 (m-30) REVERT: F 148 TYR cc_start: 0.9065 (m-80) cc_final: 0.8816 (m-80) REVERT: F 178 LYS cc_start: 0.9571 (ttpp) cc_final: 0.9272 (ttpp) REVERT: F 180 GLN cc_start: 0.8943 (pm20) cc_final: 0.8188 (pm20) REVERT: F 191 GLN cc_start: 0.9013 (tt0) cc_final: 0.8748 (tt0) REVERT: F 202 GLN cc_start: 0.9319 (mp10) cc_final: 0.8640 (mp10) REVERT: F 241 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8489 (mtm110) REVERT: F 256 PHE cc_start: 0.9445 (m-10) cc_final: 0.8978 (m-10) REVERT: F 297 PHE cc_start: 0.9566 (m-80) cc_final: 0.9359 (m-10) REVERT: F 351 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8595 (mm-30) REVERT: F 368 GLN cc_start: 0.9335 (mm110) cc_final: 0.9001 (mm110) REVERT: F 402 TYR cc_start: 0.8419 (m-80) cc_final: 0.8139 (m-80) outliers start: 77 outliers final: 52 residues processed: 394 average time/residue: 0.1376 time to fit residues: 80.9738 Evaluate side-chains 376 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 318 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain C residue 166 ASN Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 307 CYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 378 MET Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 33 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 147 optimal weight: 0.0870 chunk 110 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 184 optimal weight: 8.9990 chunk 203 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 371 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 ASN D 314 GLN D 384 ASN E 371 ASN F 314 GLN F 344 ASN F 374 HIS ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.084788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.063338 restraints weight = 54558.860| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.60 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.8501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18552 Z= 0.157 Angle : 0.660 9.645 25176 Z= 0.331 Chirality : 0.047 0.263 2994 Planarity : 0.005 0.047 3360 Dihedral : 4.258 34.349 2754 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.39 % Allowed : 22.47 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.17), residues: 2520 helix: 1.45 (0.16), residues: 1102 sheet: -0.70 (0.21), residues: 560 loop : 0.10 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 352 TYR 0.012 0.001 TYR C 486 PHE 0.022 0.002 PHE A 256 TRP 0.012 0.002 TRP B 481 HIS 0.003 0.001 HIS C 470 Details of bonding type rmsd covalent geometry : bond 0.00372 (18552) covalent geometry : angle 0.66024 (25176) hydrogen bonds : bond 0.03373 ( 942) hydrogen bonds : angle 4.47538 ( 2748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 336 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9189 (m-80) cc_final: 0.8810 (m-10) REVERT: A 202 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 243 PHE cc_start: 0.8685 (p90) cc_final: 0.8239 (p90) REVERT: A 314 GLN cc_start: 0.8579 (tp40) cc_final: 0.8216 (tm-30) REVERT: A 316 GLN cc_start: 0.8658 (mp10) cc_final: 0.8221 (mp10) REVERT: A 346 LEU cc_start: 0.9263 (mt) cc_final: 0.9015 (mm) REVERT: A 365 ASP cc_start: 0.9240 (m-30) cc_final: 0.8894 (m-30) REVERT: A 368 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8720 (tm-30) REVERT: A 391 SER cc_start: 0.9365 (t) cc_final: 0.8957 (p) REVERT: B 162 ASP cc_start: 0.8180 (m-30) cc_final: 0.7721 (m-30) REVERT: B 180 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8770 (tm-30) REVERT: B 242 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8828 (mttt) REVERT: B 246 ASP cc_start: 0.8695 (m-30) cc_final: 0.8206 (m-30) REVERT: B 256 PHE cc_start: 0.9025 (m-10) cc_final: 0.8754 (m-10) REVERT: B 312 GLU cc_start: 0.8534 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 339 ARG cc_start: 0.9180 (ttp80) cc_final: 0.8511 (mmm-85) REVERT: B 343 LYS cc_start: 0.9314 (mttp) cc_final: 0.8991 (mttm) REVERT: B 345 CYS cc_start: 0.8993 (m) cc_final: 0.8724 (m) REVERT: B 364 PHE cc_start: 0.9326 (t80) cc_final: 0.8893 (t80) REVERT: B 368 GLN cc_start: 0.8342 (mt0) cc_final: 0.7889 (mt0) REVERT: B 418 ASP cc_start: 0.7718 (m-30) cc_final: 0.7303 (m-30) REVERT: C 148 TYR cc_start: 0.8752 (m-10) cc_final: 0.8314 (m-10) REVERT: C 180 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8487 (pp30) REVERT: C 206 ARG cc_start: 0.7891 (ttp80) cc_final: 0.7613 (ttp80) REVERT: C 244 LYS cc_start: 0.9610 (mmmt) cc_final: 0.8410 (tptp) REVERT: C 247 LYS cc_start: 0.9507 (pptt) cc_final: 0.9121 (ptmm) REVERT: C 324 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8001 (tm-30) REVERT: C 339 ARG cc_start: 0.9214 (ttm-80) cc_final: 0.8715 (ttm-80) REVERT: C 364 PHE cc_start: 0.9004 (t80) cc_final: 0.8633 (t80) REVERT: C 411 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: C 482 ASP cc_start: 0.9479 (p0) cc_final: 0.9218 (p0) REVERT: D 202 GLN cc_start: 0.9038 (tt0) cc_final: 0.8678 (tm-30) REVERT: D 215 ASP cc_start: 0.8472 (t0) cc_final: 0.8194 (m-30) REVERT: D 217 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7822 (tpt-90) REVERT: D 256 PHE cc_start: 0.8804 (m-80) cc_final: 0.8560 (m-10) REVERT: D 343 LYS cc_start: 0.9260 (mtpt) cc_final: 0.8713 (mttm) REVERT: D 359 ARG cc_start: 0.8898 (ttm-80) cc_final: 0.8484 (ttm-80) REVERT: D 364 PHE cc_start: 0.8741 (t80) cc_final: 0.8523 (t80) REVERT: D 410 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8720 (mmtp) REVERT: D 438 GLU cc_start: 0.7418 (pt0) cc_final: 0.7177 (pt0) REVERT: E 164 MET cc_start: 0.8687 (mtm) cc_final: 0.8346 (mtt) REVERT: E 180 GLN cc_start: 0.8609 (pp30) cc_final: 0.8316 (pp30) REVERT: E 275 CYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8021 (m) REVERT: E 309 ASP cc_start: 0.8513 (t0) cc_final: 0.8099 (m-30) REVERT: E 339 ARG cc_start: 0.9262 (ttp80) cc_final: 0.8966 (ttp80) REVERT: E 359 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8167 (ttp80) REVERT: E 388 GLU cc_start: 0.9266 (tp30) cc_final: 0.8791 (tp30) REVERT: E 394 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8776 (tm-30) REVERT: E 406 SER cc_start: 0.9044 (m) cc_final: 0.8831 (t) REVERT: E 418 ASP cc_start: 0.8244 (m-30) cc_final: 0.7714 (m-30) REVERT: F 148 TYR cc_start: 0.9063 (m-80) cc_final: 0.8817 (m-80) REVERT: F 178 LYS cc_start: 0.9489 (ttpp) cc_final: 0.9201 (ttpp) REVERT: F 180 GLN cc_start: 0.8617 (pm20) cc_final: 0.7875 (pm20) REVERT: F 191 GLN cc_start: 0.8911 (tt0) cc_final: 0.8634 (tt0) REVERT: F 202 GLN cc_start: 0.9179 (mp10) cc_final: 0.8534 (mp10) REVERT: F 241 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8327 (mtm110) REVERT: F 256 PHE cc_start: 0.9436 (m-10) cc_final: 0.8967 (m-10) REVERT: F 402 TYR cc_start: 0.8317 (m-80) cc_final: 0.7989 (m-80) outliers start: 78 outliers final: 57 residues processed: 391 average time/residue: 0.1380 time to fit residues: 79.9775 Evaluate side-chains 379 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 151 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 141 optimal weight: 20.0000 chunk 160 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN ** F 422 GLN ** 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 = 0.3501 r_free = 0.3501 target = 0.085034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.063112 restraints weight = 55320.727| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.77 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.8718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18552 Z= 0.145 Angle : 0.669 11.258 25176 Z= 0.331 Chirality : 0.047 0.243 2994 Planarity : 0.005 0.053 3360 Dihedral : 4.189 34.026 2754 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.11 % Allowed : 23.76 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.17), residues: 2520 helix: 1.44 (0.16), residues: 1108 sheet: -0.65 (0.21), residues: 560 loop : 0.10 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 491 TYR 0.016 0.001 TYR C 486 PHE 0.014 0.002 PHE B 297 TRP 0.011 0.002 TRP B 481 HIS 0.002 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00348 (18552) covalent geometry : angle 0.66892 (25176) hydrogen bonds : bond 0.03222 ( 942) hydrogen bonds : angle 4.40330 ( 2748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 333 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9215 (m-80) cc_final: 0.8842 (m-10) REVERT: A 197 GLN cc_start: 0.8963 (tp40) cc_final: 0.8761 (tp40) REVERT: A 202 GLN cc_start: 0.8974 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 215 ASP cc_start: 0.8418 (t0) cc_final: 0.8133 (t0) REVERT: A 243 PHE cc_start: 0.8719 (p90) cc_final: 0.8295 (p90) REVERT: A 314 GLN cc_start: 0.8581 (tp40) cc_final: 0.8273 (tm-30) REVERT: A 365 ASP cc_start: 0.9251 (m-30) cc_final: 0.8882 (m-30) REVERT: A 368 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8559 (tm-30) REVERT: A 391 SER cc_start: 0.9371 (t) cc_final: 0.8976 (p) REVERT: A 457 ILE cc_start: 0.8866 (mm) cc_final: 0.8641 (mm) REVERT: B 162 ASP cc_start: 0.8205 (m-30) cc_final: 0.7751 (m-30) REVERT: B 180 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8734 (tm-30) REVERT: B 242 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8840 (mttt) REVERT: B 256 PHE cc_start: 0.8993 (m-10) cc_final: 0.8730 (m-10) REVERT: B 312 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7987 (mm-30) REVERT: B 339 ARG cc_start: 0.9177 (ttp80) cc_final: 0.8297 (mmm-85) REVERT: B 343 LYS cc_start: 0.9307 (mttp) cc_final: 0.9028 (mttp) REVERT: B 364 PHE cc_start: 0.9315 (t80) cc_final: 0.8976 (t80) REVERT: B 368 GLN cc_start: 0.8317 (mt0) cc_final: 0.7921 (mt0) REVERT: B 416 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8249 (m) REVERT: B 418 ASP cc_start: 0.7697 (m-30) cc_final: 0.7239 (m-30) REVERT: C 148 TYR cc_start: 0.8770 (m-10) cc_final: 0.8349 (m-10) REVERT: C 180 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8414 (pp30) REVERT: C 206 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7625 (ttp80) REVERT: C 244 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9015 (tptp) REVERT: C 324 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 339 ARG cc_start: 0.9245 (ttm-80) cc_final: 0.8718 (ttm-80) REVERT: C 347 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8488 (ttm110) REVERT: C 364 PHE cc_start: 0.9000 (t80) cc_final: 0.8766 (t80) REVERT: C 396 MET cc_start: 0.8543 (tpp) cc_final: 0.8108 (mtt) REVERT: C 399 MET cc_start: 0.9458 (ptp) cc_final: 0.9004 (ppp) REVERT: C 411 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (mp0) REVERT: C 482 ASP cc_start: 0.9472 (p0) cc_final: 0.9227 (p0) REVERT: D 202 GLN cc_start: 0.9025 (tt0) cc_final: 0.8694 (tm-30) REVERT: D 215 ASP cc_start: 0.8508 (t0) cc_final: 0.7607 (m-30) REVERT: D 217 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7835 (tpt-90) REVERT: D 240 ILE cc_start: 0.8337 (mm) cc_final: 0.8112 (mm) REVERT: D 256 PHE cc_start: 0.8846 (m-80) cc_final: 0.8616 (m-10) REVERT: D 343 LYS cc_start: 0.9306 (mtpt) cc_final: 0.8772 (mttm) REVERT: D 359 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8660 (ttm110) REVERT: D 364 PHE cc_start: 0.8759 (t80) cc_final: 0.8387 (t80) REVERT: D 410 LYS cc_start: 0.9243 (mmtm) cc_final: 0.8748 (mmtp) REVERT: D 438 GLU cc_start: 0.7471 (pt0) cc_final: 0.7220 (pt0) REVERT: E 148 TYR cc_start: 0.8680 (m-10) cc_final: 0.8429 (m-10) REVERT: E 164 MET cc_start: 0.8697 (mtm) cc_final: 0.8342 (mtt) REVERT: E 180 GLN cc_start: 0.8706 (pp30) cc_final: 0.8368 (pp30) REVERT: E 256 PHE cc_start: 0.8872 (m-10) cc_final: 0.8630 (m-10) REVERT: E 275 CYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8117 (m) REVERT: E 309 ASP cc_start: 0.8516 (t0) cc_final: 0.8012 (m-30) REVERT: E 339 ARG cc_start: 0.9289 (ttp80) cc_final: 0.8990 (ttp80) REVERT: E 359 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8101 (ttp80) REVERT: E 388 GLU cc_start: 0.9264 (tp30) cc_final: 0.8727 (tp30) REVERT: E 394 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8785 (tm-30) REVERT: E 406 SER cc_start: 0.9052 (m) cc_final: 0.8842 (t) REVERT: E 418 ASP cc_start: 0.8218 (m-30) cc_final: 0.7635 (m-30) REVERT: F 148 TYR cc_start: 0.9054 (m-80) cc_final: 0.8825 (m-80) REVERT: F 178 LYS cc_start: 0.9478 (ttpp) cc_final: 0.9208 (ttpp) REVERT: F 180 GLN cc_start: 0.8601 (pm20) cc_final: 0.7852 (pm20) REVERT: F 191 GLN cc_start: 0.8882 (tt0) cc_final: 0.8598 (tt0) REVERT: F 202 GLN cc_start: 0.9173 (mp10) cc_final: 0.8531 (mp10) REVERT: F 241 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8473 (mtm110) REVERT: F 256 PHE cc_start: 0.9448 (m-10) cc_final: 0.9169 (m-10) REVERT: F 399 MET cc_start: 0.9462 (ptp) cc_final: 0.8808 (ppp) REVERT: F 402 TYR cc_start: 0.8389 (m-80) cc_final: 0.8046 (m-80) outliers start: 73 outliers final: 55 residues processed: 385 average time/residue: 0.1369 time to fit residues: 78.8682 Evaluate side-chains 372 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 309 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 416 SER Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 308 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 133 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 223 optimal weight: 5.9990 chunk 42 optimal weight: 120.0000 chunk 1 optimal weight: 20.0000 chunk 120 optimal weight: 0.0870 chunk 88 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 46 optimal weight: 50.0000 overall best weight: 5.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 384 ASN ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** 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 = 0.3496 r_free = 0.3496 target = 0.084785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062938 restraints weight = 55192.056| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.72 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.9004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18552 Z= 0.161 Angle : 0.679 11.248 25176 Z= 0.338 Chirality : 0.047 0.223 2994 Planarity : 0.004 0.048 3360 Dihedral : 4.176 33.979 2754 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.00 % Allowed : 24.21 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2520 helix: 1.40 (0.16), residues: 1108 sheet: -0.61 (0.21), residues: 560 loop : 0.09 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 491 TYR 0.015 0.001 TYR E 148 PHE 0.019 0.002 PHE F 364 TRP 0.011 0.001 TRP B 481 HIS 0.002 0.001 HIS F 319 Details of bonding type rmsd covalent geometry : bond 0.00383 (18552) covalent geometry : angle 0.67934 (25176) hydrogen bonds : bond 0.03268 ( 942) hydrogen bonds : angle 4.42320 ( 2748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 324 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9278 (m-80) cc_final: 0.8811 (m-10) REVERT: A 197 GLN cc_start: 0.9087 (tp40) cc_final: 0.8802 (tp40) REVERT: A 202 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8817 (tm-30) REVERT: A 215 ASP cc_start: 0.8443 (t0) cc_final: 0.8033 (t0) REVERT: A 243 PHE cc_start: 0.8744 (p90) cc_final: 0.8310 (p90) REVERT: A 343 LYS cc_start: 0.9540 (ttmt) cc_final: 0.9057 (ttmm) REVERT: A 346 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9070 (mm) REVERT: A 365 ASP cc_start: 0.9288 (m-30) cc_final: 0.8652 (m-30) REVERT: A 368 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8717 (tm-30) REVERT: A 378 MET cc_start: 0.8465 (ptp) cc_final: 0.8087 (ptp) REVERT: A 391 SER cc_start: 0.9405 (t) cc_final: 0.9012 (p) REVERT: A 457 ILE cc_start: 0.8877 (mm) cc_final: 0.8647 (mm) REVERT: B 162 ASP cc_start: 0.8270 (m-30) cc_final: 0.7842 (m-30) REVERT: B 180 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8713 (tm-30) REVERT: B 242 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8895 (mttt) REVERT: B 256 PHE cc_start: 0.9042 (m-10) cc_final: 0.8779 (m-10) REVERT: B 312 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8151 (mm-30) REVERT: B 339 ARG cc_start: 0.9169 (ttp80) cc_final: 0.8091 (mmm-85) REVERT: B 343 LYS cc_start: 0.9295 (mttp) cc_final: 0.8889 (mttp) REVERT: B 364 PHE cc_start: 0.9365 (t80) cc_final: 0.9012 (t80) REVERT: B 368 GLN cc_start: 0.8330 (mt0) cc_final: 0.7976 (mt0) REVERT: B 418 ASP cc_start: 0.7771 (m-30) cc_final: 0.7295 (m-30) REVERT: C 148 TYR cc_start: 0.8779 (m-10) cc_final: 0.8393 (m-10) REVERT: C 180 GLN cc_start: 0.8602 (pp30) cc_final: 0.8387 (pp30) REVERT: C 206 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7359 (ttp80) REVERT: C 339 ARG cc_start: 0.9275 (ttm-80) cc_final: 0.8692 (ttm-80) REVERT: C 343 LYS cc_start: 0.9435 (mttm) cc_final: 0.9004 (mmtt) REVERT: C 347 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8486 (ttm110) REVERT: C 364 PHE cc_start: 0.9128 (t80) cc_final: 0.8813 (t80) REVERT: C 411 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: C 482 ASP cc_start: 0.9479 (p0) cc_final: 0.9223 (p0) REVERT: D 202 GLN cc_start: 0.8955 (tt0) cc_final: 0.8639 (tm-30) REVERT: D 215 ASP cc_start: 0.8484 (t0) cc_final: 0.7571 (m-30) REVERT: D 217 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7875 (tpt-90) REVERT: D 240 ILE cc_start: 0.8400 (mm) cc_final: 0.8199 (mm) REVERT: D 256 PHE cc_start: 0.8924 (m-80) cc_final: 0.8701 (m-10) REVERT: D 343 LYS cc_start: 0.9298 (mtpt) cc_final: 0.8766 (mttm) REVERT: D 364 PHE cc_start: 0.8842 (t80) cc_final: 0.8542 (t80) REVERT: D 391 SER cc_start: 0.9567 (t) cc_final: 0.8998 (p) REVERT: D 392 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9133 (tpp80) REVERT: D 410 LYS cc_start: 0.9277 (mmtm) cc_final: 0.8748 (mmtp) REVERT: D 438 GLU cc_start: 0.7496 (pt0) cc_final: 0.7243 (pt0) REVERT: D 487 TYR cc_start: 0.8875 (m-80) cc_final: 0.8591 (m-80) REVERT: E 164 MET cc_start: 0.8737 (mtm) cc_final: 0.8370 (mtt) REVERT: E 180 GLN cc_start: 0.8736 (pp30) cc_final: 0.8372 (pp30) REVERT: E 256 PHE cc_start: 0.8923 (m-10) cc_final: 0.8664 (m-10) REVERT: E 275 CYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8150 (m) REVERT: E 309 ASP cc_start: 0.8513 (t0) cc_final: 0.7993 (m-30) REVERT: E 339 ARG cc_start: 0.9311 (ttp80) cc_final: 0.9015 (ttp80) REVERT: E 359 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8083 (ttp80) REVERT: E 372 THR cc_start: 0.9488 (m) cc_final: 0.9282 (p) REVERT: E 388 GLU cc_start: 0.9240 (tp30) cc_final: 0.8721 (tp30) REVERT: E 394 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8797 (tm-30) REVERT: E 418 ASP cc_start: 0.8257 (m-30) cc_final: 0.7642 (m-30) REVERT: F 178 LYS cc_start: 0.9458 (ttpp) cc_final: 0.9191 (ttpp) REVERT: F 180 GLN cc_start: 0.8628 (pm20) cc_final: 0.7906 (pm20) REVERT: F 191 GLN cc_start: 0.8913 (tt0) cc_final: 0.8635 (tt0) REVERT: F 202 GLN cc_start: 0.9150 (mp10) cc_final: 0.8499 (mp10) REVERT: F 210 SER cc_start: 0.9590 (m) cc_final: 0.9285 (p) REVERT: F 241 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8466 (mtm110) REVERT: F 256 PHE cc_start: 0.9458 (m-10) cc_final: 0.9174 (m-10) REVERT: F 314 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8224 (tm-30) REVERT: F 399 MET cc_start: 0.9432 (ptp) cc_final: 0.8789 (ppp) REVERT: F 402 TYR cc_start: 0.8345 (m-80) cc_final: 0.7986 (m-80) REVERT: F 453 PHE cc_start: 0.8616 (m-80) cc_final: 0.8404 (m-80) outliers start: 71 outliers final: 57 residues processed: 377 average time/residue: 0.1316 time to fit residues: 75.3176 Evaluate side-chains 371 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 60 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 120.0000 chunk 17 optimal weight: 9.9990 chunk 129 optimal weight: 50.0000 chunk 20 optimal weight: 8.9990 chunk 249 optimal weight: 20.0000 chunk 237 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 overall best weight: 5.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 ASN D 225 ASN F 368 GLN ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.084427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.062659 restraints weight = 55526.957| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.71 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.9214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18552 Z= 0.167 Angle : 0.704 12.320 25176 Z= 0.348 Chirality : 0.048 0.248 2994 Planarity : 0.005 0.048 3360 Dihedral : 4.194 33.926 2754 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.94 % Allowed : 24.83 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.17), residues: 2520 helix: 1.36 (0.16), residues: 1108 sheet: -0.62 (0.21), residues: 564 loop : 0.06 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 352 TYR 0.017 0.001 TYR E 148 PHE 0.031 0.002 PHE B 243 TRP 0.010 0.001 TRP B 481 HIS 0.002 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00400 (18552) covalent geometry : angle 0.70399 (25176) hydrogen bonds : bond 0.03236 ( 942) hydrogen bonds : angle 4.42628 ( 2748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 319 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 PHE cc_start: 0.9283 (m-80) cc_final: 0.8686 (m-10) REVERT: A 193 MET cc_start: 0.9243 (tpt) cc_final: 0.9022 (tpp) REVERT: A 197 GLN cc_start: 0.9108 (tp40) cc_final: 0.8856 (tp40) REVERT: A 202 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8893 (tm-30) REVERT: A 215 ASP cc_start: 0.8525 (t0) cc_final: 0.8042 (t0) REVERT: A 243 PHE cc_start: 0.8794 (p90) cc_final: 0.8348 (p90) REVERT: A 343 LYS cc_start: 0.9548 (ttmt) cc_final: 0.9050 (ttmm) REVERT: A 346 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9093 (mm) REVERT: A 365 ASP cc_start: 0.9284 (m-30) cc_final: 0.8639 (m-30) REVERT: A 368 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8733 (tm-30) REVERT: A 378 MET cc_start: 0.8468 (ptp) cc_final: 0.8022 (ptp) REVERT: A 391 SER cc_start: 0.9428 (t) cc_final: 0.9011 (p) REVERT: A 457 ILE cc_start: 0.8963 (mm) cc_final: 0.8741 (mm) REVERT: B 162 ASP cc_start: 0.8303 (m-30) cc_final: 0.7882 (m-30) REVERT: B 180 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8691 (tm-30) REVERT: B 242 LYS cc_start: 0.9240 (OUTLIER) cc_final: 0.8973 (mttt) REVERT: B 256 PHE cc_start: 0.9040 (m-10) cc_final: 0.8785 (m-10) REVERT: B 312 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8115 (mm-30) REVERT: B 339 ARG cc_start: 0.9161 (ttp80) cc_final: 0.8377 (mmm-85) REVERT: B 343 LYS cc_start: 0.9327 (mttp) cc_final: 0.8900 (mttm) REVERT: B 364 PHE cc_start: 0.9367 (t80) cc_final: 0.8953 (t80) REVERT: B 368 GLN cc_start: 0.8264 (mt0) cc_final: 0.7834 (mt0) REVERT: B 402 TYR cc_start: 0.8690 (m-80) cc_final: 0.8384 (m-80) REVERT: B 418 ASP cc_start: 0.7850 (m-30) cc_final: 0.7382 (m-30) REVERT: C 148 TYR cc_start: 0.8796 (m-10) cc_final: 0.8423 (m-10) REVERT: C 180 GLN cc_start: 0.8569 (pp30) cc_final: 0.8348 (pp30) REVERT: C 206 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7412 (ttp80) REVERT: C 324 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 339 ARG cc_start: 0.9296 (ttm-80) cc_final: 0.8645 (ttm-80) REVERT: C 343 LYS cc_start: 0.9427 (mttm) cc_final: 0.9055 (mmtm) REVERT: C 347 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8432 (ttm110) REVERT: C 364 PHE cc_start: 0.9113 (t80) cc_final: 0.8815 (t80) REVERT: C 399 MET cc_start: 0.9455 (ptp) cc_final: 0.9013 (ppp) REVERT: C 411 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: C 482 ASP cc_start: 0.9474 (p0) cc_final: 0.9204 (p0) REVERT: D 202 GLN cc_start: 0.9009 (tt0) cc_final: 0.8728 (tm-30) REVERT: D 215 ASP cc_start: 0.8388 (t0) cc_final: 0.7080 (m-30) REVERT: D 217 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7869 (tpt-90) REVERT: D 240 ILE cc_start: 0.8578 (mm) cc_final: 0.8343 (mm) REVERT: D 256 PHE cc_start: 0.8983 (m-80) cc_final: 0.8767 (m-10) REVERT: D 343 LYS cc_start: 0.9302 (mtpt) cc_final: 0.8762 (mttm) REVERT: D 359 ARG cc_start: 0.9090 (ttm-80) cc_final: 0.8696 (ttm110) REVERT: D 364 PHE cc_start: 0.8873 (t80) cc_final: 0.8622 (t80) REVERT: D 391 SER cc_start: 0.9554 (t) cc_final: 0.9025 (p) REVERT: D 392 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.9158 (tpp80) REVERT: D 410 LYS cc_start: 0.9287 (mmtm) cc_final: 0.8760 (mmtp) REVERT: D 487 TYR cc_start: 0.8882 (m-80) cc_final: 0.8598 (m-80) REVERT: E 164 MET cc_start: 0.8773 (mtm) cc_final: 0.8410 (mtt) REVERT: E 180 GLN cc_start: 0.8753 (pp30) cc_final: 0.8431 (pp30) REVERT: E 256 PHE cc_start: 0.8938 (m-10) cc_final: 0.8711 (m-10) REVERT: E 275 CYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8115 (m) REVERT: E 309 ASP cc_start: 0.8510 (t0) cc_final: 0.7938 (m-30) REVERT: E 339 ARG cc_start: 0.9335 (ttp80) cc_final: 0.9051 (ttp80) REVERT: E 359 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8066 (ttp80) REVERT: E 388 GLU cc_start: 0.9216 (tp30) cc_final: 0.8674 (tp30) REVERT: E 394 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8743 (tm-30) REVERT: E 399 MET cc_start: 0.8769 (ptp) cc_final: 0.8494 (ptp) REVERT: E 418 ASP cc_start: 0.8334 (m-30) cc_final: 0.7710 (m-30) REVERT: F 178 LYS cc_start: 0.9457 (ttpp) cc_final: 0.9234 (ttpp) REVERT: F 180 GLN cc_start: 0.8640 (pm20) cc_final: 0.7943 (pm20) REVERT: F 191 GLN cc_start: 0.8927 (tt0) cc_final: 0.8709 (tt0) REVERT: F 206 ARG cc_start: 0.8186 (mmm160) cc_final: 0.7789 (mmp-170) REVERT: F 210 SER cc_start: 0.9590 (m) cc_final: 0.9220 (p) REVERT: F 241 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8486 (mtm110) REVERT: F 256 PHE cc_start: 0.9445 (m-10) cc_final: 0.9154 (m-10) REVERT: F 370 MET cc_start: 0.9116 (mtm) cc_final: 0.8804 (ttm) REVERT: F 399 MET cc_start: 0.9438 (ptp) cc_final: 0.8788 (ppp) REVERT: F 402 TYR cc_start: 0.8414 (m-80) cc_final: 0.8004 (m-80) REVERT: F 453 PHE cc_start: 0.8601 (m-80) cc_final: 0.8389 (m-80) outliers start: 70 outliers final: 59 residues processed: 371 average time/residue: 0.1341 time to fit residues: 74.8947 Evaluate side-chains 376 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 310 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 347 ARG Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 402 TYR Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 420 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 197 GLN Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 217 ARG Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain E residue 214 CYS Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 275 CYS Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 341 LEU Chi-restraints excluded: chain E residue 463 HIS Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 241 ARG Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 298 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain F residue 396 MET Chi-restraints excluded: chain F residue 434 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 463 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 162 optimal weight: 10.0000 chunk 6 optimal weight: 50.0000 chunk 250 optimal weight: 5.9990 chunk 17 optimal weight: 40.0000 chunk 127 optimal weight: 30.0000 chunk 225 optimal weight: 1.9990 chunk 232 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 GLN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 422 GLN ** 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 = 0.3505 r_free = 0.3505 target = 0.085371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064048 restraints weight = 54673.949| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 4.66 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.9348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18552 Z= 0.134 Angle : 0.699 12.435 25176 Z= 0.343 Chirality : 0.048 0.248 2994 Planarity : 0.005 0.048 3360 Dihedral : 4.129 33.599 2754 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.55 % Allowed : 25.39 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.17), residues: 2520 helix: 1.38 (0.16), residues: 1108 sheet: -0.59 (0.22), residues: 548 loop : 0.00 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 491 TYR 0.015 0.001 TYR E 148 PHE 0.029 0.002 PHE F 364 TRP 0.009 0.002 TRP E 481 HIS 0.002 0.000 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00325 (18552) covalent geometry : angle 0.69942 (25176) hydrogen bonds : bond 0.03147 ( 942) hydrogen bonds : angle 4.36255 ( 2748) =============================================================================== Job complete usr+sys time: 3491.12 seconds wall clock time: 60 minutes 48.24 seconds (3648.24 seconds total)