Starting phenix.real_space_refine on Thu Mar 5 04:20:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6r_25725/03_2026/7t6r_25725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6r_25725/03_2026/7t6r_25725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t6r_25725/03_2026/7t6r_25725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6r_25725/03_2026/7t6r_25725.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t6r_25725/03_2026/7t6r_25725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6r_25725/03_2026/7t6r_25725.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.033 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 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 4.00, per 1000 atoms: 0.21 Number of scatterers: 19412 At special positions: 0 Unit cell: (138.61, 138.61, 121.18, 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 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 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: 1.62 Conformation dependent library (CDL) restraints added in 847.2 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 8 sheets defined 65.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 removed outlier: 3.557A pdb=" N ASP A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 47 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 57 through 67 removed outlier: 3.940A pdb=" N ASN A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 107 removed outlier: 4.239A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.735A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.914A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 175 through 185 removed outlier: 3.525A pdb=" N VAL A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.771A pdb=" N ASN A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 251 Processing helix chain 'A' and resid 252 through 263 removed outlier: 3.806A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 310 through 324 removed outlier: 4.139A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 removed outlier: 3.538A pdb=" N TYR A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 410 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.503A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 446 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.581A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 510 removed outlier: 4.180A pdb=" N LEU A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N MET A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.609A pdb=" N LEU A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.584A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 removed outlier: 3.848A pdb=" N ARG A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 604 removed outlier: 3.806A pdb=" N VAL A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 removed outlier: 3.608A pdb=" N SER B 47 " --> pdb=" O ARG B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 56 Processing helix chain 'B' and resid 57 through 67 removed outlier: 3.973A pdb=" N ASN B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 107 removed outlier: 4.284A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.725A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.959A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 185 removed outlier: 3.660A pdb=" N VAL B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.777A pdb=" N ASN B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 251 Processing helix chain 'B' and resid 252 through 263 removed outlier: 3.818A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 312 through 324 removed outlier: 3.523A pdb=" N TYR B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 removed outlier: 3.500A pdb=" N TYR B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 410 Proline residue: B 405 - end of helix Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.518A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 446 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.615A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 510 removed outlier: 4.165A pdb=" N LEU B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N MET B 491 " --> pdb=" O PHE B 487 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.651A pdb=" N LEU B 538 " --> pdb=" O PHE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.593A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 585 removed outlier: 4.113A pdb=" N ASN B 572 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG B 584 " --> pdb=" O ASP B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 604 removed outlier: 3.818A pdb=" N VAL B 598 " --> pdb=" O ARG B 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 57 through 67 removed outlier: 3.948A pdb=" N ASN C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.288A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.759A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.848A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 Processing helix chain 'C' and resid 175 through 185 removed outlier: 3.705A pdb=" N VAL C 179 " --> pdb=" O SER C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 197 removed outlier: 3.860A pdb=" N ASN C 197 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 206 removed outlier: 3.544A pdb=" N ILE C 202 " --> pdb=" O THR C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.808A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.140A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 removed outlier: 3.530A pdb=" N TYR C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.519A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 446 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.624A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 510 removed outlier: 4.187A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N MET C 491 " --> pdb=" O PHE C 487 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.586A pdb=" N LEU C 538 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.590A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 585 removed outlier: 4.048A pdb=" N ASN C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG C 584 " --> pdb=" O ASP C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 585 through 604 removed outlier: 3.804A pdb=" N VAL C 598 " --> pdb=" O ARG C 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.591A pdb=" N SER D 47 " --> pdb=" O ARG D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'D' and resid 57 through 67 removed outlier: 3.917A pdb=" N ASN D 67 " --> pdb=" O ILE D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.275A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.738A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.841A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.527A pdb=" N VAL D 179 " --> pdb=" O SER D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 197 removed outlier: 3.785A pdb=" N ASN D 197 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 206 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 231 through 235 removed outlier: 3.504A pdb=" N LEU D 234 " --> pdb=" O SER D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 252 through 262 removed outlier: 4.008A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 removed outlier: 3.503A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 4.127A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 removed outlier: 3.531A pdb=" N TYR D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 410 Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.517A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 446 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.579A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 510 removed outlier: 4.170A pdb=" N LEU D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET D 491 " --> pdb=" O PHE D 487 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.687A pdb=" N LEU D 538 " --> pdb=" O PHE D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.577A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 585 removed outlier: 4.045A pdb=" N ASN D 572 " --> pdb=" O LEU D 568 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D 584 " --> pdb=" O ASP D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 604 removed outlier: 3.821A pdb=" N VAL D 598 " --> pdb=" O ARG D 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.835A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.842A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.842A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.844A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1086 hydrogen bonds defined for protein. 3177 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: 2.52 Time building geometry restraints manager: 2.19 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: 4991 1.34 - 1.45: 3870 1.45 - 1.57: 10771 1.57 - 1.69: 0 1.69 - 1.81: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C GLU D 113 " pdb=" N PRO D 114 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.59e+01 bond pdb=" C GLU A 113 " pdb=" N PRO A 114 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.54e+01 bond pdb=" C GLU B 113 " pdb=" N PRO B 114 " ideal model delta sigma weight residual 1.337 1.386 -0.049 1.24e-02 6.50e+03 1.53e+01 bond pdb=" C GLU C 113 " pdb=" N PRO C 114 " ideal model delta sigma weight residual 1.337 1.385 -0.048 1.24e-02 6.50e+03 1.52e+01 bond pdb=" N ASP C 627 " pdb=" CA ASP C 627 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.72e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 25913 2.44 - 4.87: 834 4.87 - 7.31: 157 7.31 - 9.75: 47 9.75 - 12.18: 13 Bond angle restraints: 26964 Sorted by residual: angle pdb=" C LEU D 604 " pdb=" N GLU D 605 " pdb=" CA GLU D 605 " ideal model delta sigma weight residual 121.54 133.51 -11.97 1.91e+00 2.74e-01 3.93e+01 angle pdb=" C LEU A 604 " pdb=" N GLU A 605 " pdb=" CA GLU A 605 " ideal model delta sigma weight residual 121.54 133.32 -11.78 1.91e+00 2.74e-01 3.81e+01 angle pdb=" C LEU C 604 " pdb=" N GLU C 605 " pdb=" CA GLU C 605 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C LEU B 604 " pdb=" N GLU B 605 " pdb=" CA GLU B 605 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C GLY D 626 " pdb=" N ASP D 627 " pdb=" CA ASP D 627 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 10534 16.65 - 33.31: 1013 33.31 - 49.96: 202 49.96 - 66.61: 39 66.61 - 83.26: 24 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA ILE C 510 " pdb=" C ILE C 510 " pdb=" N THR C 511 " pdb=" CA THR C 511 " ideal model delta harmonic sigma weight residual 180.00 147.14 32.86 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA ILE D 510 " pdb=" C ILE D 510 " pdb=" N THR D 511 " pdb=" CA THR D 511 " ideal model delta harmonic sigma weight residual 180.00 147.19 32.81 0 5.00e+00 4.00e-02 4.31e+01 dihedral pdb=" CA ILE A 510 " pdb=" C ILE A 510 " pdb=" N THR A 511 " pdb=" CA THR A 511 " ideal model delta harmonic sigma weight residual 180.00 147.25 32.75 0 5.00e+00 4.00e-02 4.29e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2585 0.074 - 0.148: 395 0.148 - 0.222: 77 0.222 - 0.296: 11 0.296 - 0.369: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CB VAL C 297 " pdb=" CA VAL C 297 " pdb=" CG1 VAL C 297 " pdb=" CG2 VAL C 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB VAL D 297 " pdb=" CA VAL D 297 " pdb=" CG1 VAL D 297 " pdb=" CG2 VAL D 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.34e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 511 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.50e+00 pdb=" C THR D 511 " 0.050 2.00e-02 2.50e+03 pdb=" O THR D 511 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE D 512 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 511 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.48e+00 pdb=" C THR B 511 " -0.050 2.00e-02 2.50e+03 pdb=" O THR B 511 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE B 512 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 511 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C THR A 511 " -0.050 2.00e-02 2.50e+03 pdb=" O THR A 511 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 512 " 0.017 2.00e-02 2.50e+03 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6243 2.85 - 3.36: 18010 3.36 - 3.87: 32961 3.87 - 4.39: 38676 4.39 - 4.90: 65671 Nonbonded interactions: 161561 Sorted by model distance: nonbonded pdb=" O PRO D 544 " pdb=" OH TYR D 555 " model vdw 2.335 3.040 nonbonded pdb=" O PRO C 544 " pdb=" OH TYR C 555 " model vdw 2.337 3.040 nonbonded pdb=" O PRO A 544 " pdb=" OH TYR A 555 " model vdw 2.344 3.040 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.345 3.040 nonbonded pdb=" OE1 GLU A 403 " pdb=" OH TYR A 415 " model vdw 2.359 3.040 ... (remaining 161556 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.520 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: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.140 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.005 0.063 19860 Z= 0.267 Angle : 1.072 12.183 26964 Z= 0.567 Chirality : 0.058 0.369 3072 Planarity : 0.008 0.063 3416 Dihedral : 14.253 83.263 7236 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.26 (0.13), residues: 2408 helix: -2.09 (0.10), residues: 1484 sheet: -2.20 (0.52), residues: 64 loop : -1.96 (0.18), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 139 TYR 0.025 0.002 TYR C 621 PHE 0.039 0.002 PHE C 456 TRP 0.019 0.002 TRP D 583 HIS 0.010 0.001 HIS D 157 Details of bonding type rmsd covalent geometry : bond 0.00519 (19860) covalent geometry : angle 1.07158 (26964) hydrogen bonds : bond 0.15804 ( 1086) hydrogen bonds : angle 6.72315 ( 3177) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.711 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.6287 time to fit residues: 191.8566 Evaluate side-chains 193 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 185 HIS ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 369 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 GLN C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS C 261 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 GLN D 185 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.160420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.128657 restraints weight = 23032.198| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.67 r_work: 0.3388 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19860 Z= 0.138 Angle : 0.585 7.909 26964 Z= 0.305 Chirality : 0.040 0.137 3072 Planarity : 0.005 0.044 3416 Dihedral : 4.872 26.024 2644 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.91 % Allowed : 9.73 % Favored : 89.36 % 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 are not related in a simple way. whole: -1.15 (0.15), residues: 2408 helix: -0.12 (0.12), residues: 1508 sheet: -1.81 (0.46), residues: 96 loop : -1.71 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 43 TYR 0.014 0.001 TYR D 555 PHE 0.015 0.001 PHE D 537 TRP 0.009 0.001 TRP D 321 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00315 (19860) covalent geometry : angle 0.58462 (26964) hydrogen bonds : bond 0.04169 ( 1086) hydrogen bonds : angle 4.30946 ( 3177) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 0.686 Fit side-chains REVERT: A 176 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 215 MET cc_start: 0.9106 (tpt) cc_final: 0.8844 (tpt) REVERT: A 487 PHE cc_start: 0.7925 (m-10) cc_final: 0.7594 (m-10) REVERT: B 290 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.5505 (pt) REVERT: B 487 PHE cc_start: 0.7855 (m-10) cc_final: 0.7495 (m-10) REVERT: B 554 MET cc_start: 0.8197 (tpt) cc_final: 0.7974 (tpt) REVERT: C 290 LEU cc_start: 0.6607 (OUTLIER) cc_final: 0.5535 (pt) REVERT: C 487 PHE cc_start: 0.7814 (m-10) cc_final: 0.7478 (m-10) REVERT: D 487 PHE cc_start: 0.7876 (m-10) cc_final: 0.7590 (m-10) outliers start: 19 outliers final: 4 residues processed: 234 average time/residue: 0.6329 time to fit residues: 165.8397 Evaluate side-chains 189 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 189 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 0.3980 chunk 161 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 261 GLN A 446 ASN B 185 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 446 ASN C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 446 ASN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS D 192 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 446 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.156229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123856 restraints weight = 23074.732| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.73 r_work: 0.3304 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19860 Z= 0.142 Angle : 0.568 8.255 26964 Z= 0.296 Chirality : 0.040 0.143 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.638 25.115 2644 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.81 % Allowed : 13.50 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.16), residues: 2408 helix: 0.71 (0.13), residues: 1508 sheet: -2.21 (0.42), residues: 116 loop : -1.53 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 146 TYR 0.011 0.001 TYR C 216 PHE 0.013 0.001 PHE A 537 TRP 0.009 0.001 TRP C 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00332 (19860) covalent geometry : angle 0.56840 (26964) hydrogen bonds : bond 0.04078 ( 1086) hydrogen bonds : angle 4.10823 ( 3177) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.613 Fit side-chains REVERT: A 99 MET cc_start: 0.7391 (mtm) cc_final: 0.7152 (mtp) REVERT: A 146 ARG cc_start: 0.8172 (mtp85) cc_final: 0.7696 (mmm-85) REVERT: A 487 PHE cc_start: 0.8131 (m-10) cc_final: 0.7819 (m-10) REVERT: B 146 ARG cc_start: 0.8159 (mtp85) cc_final: 0.7675 (mmm-85) REVERT: B 177 GLU cc_start: 0.7370 (tp30) cc_final: 0.7169 (tp30) REVERT: B 290 LEU cc_start: 0.6763 (tp) cc_final: 0.5638 (pt) REVERT: B 487 PHE cc_start: 0.8112 (m-10) cc_final: 0.7802 (m-10) REVERT: B 554 MET cc_start: 0.8327 (tpt) cc_final: 0.8118 (tpt) REVERT: C 290 LEU cc_start: 0.6754 (tp) cc_final: 0.5631 (pt) REVERT: C 487 PHE cc_start: 0.8070 (m-10) cc_final: 0.7756 (m-10) REVERT: D 146 ARG cc_start: 0.8165 (mtp85) cc_final: 0.7683 (mmm-85) outliers start: 38 outliers final: 9 residues processed: 221 average time/residue: 0.5660 time to fit residues: 140.8683 Evaluate side-chains 196 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 187 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 451 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 5.9990 chunk 91 optimal weight: 0.0570 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 117 optimal weight: 0.0980 chunk 108 optimal weight: 0.0770 chunk 79 optimal weight: 0.0050 chunk 77 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.1670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 369 GLN B 51 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 201 HIS C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 369 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.165984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136706 restraints weight = 22693.991| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.60 r_work: 0.3385 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19860 Z= 0.095 Angle : 0.517 11.232 26964 Z= 0.265 Chirality : 0.038 0.124 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.333 26.420 2644 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.29 % Allowed : 14.89 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2408 helix: 1.16 (0.13), residues: 1508 sheet: -2.23 (0.42), residues: 116 loop : -1.34 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.011 0.001 TYR D 555 PHE 0.010 0.001 PHE A 611 TRP 0.011 0.001 TRP A 593 HIS 0.002 0.000 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00193 (19860) covalent geometry : angle 0.51663 (26964) hydrogen bonds : bond 0.03278 ( 1086) hydrogen bonds : angle 3.85535 ( 3177) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.587 Fit side-chains REVERT: A 38 MET cc_start: 0.9047 (mmm) cc_final: 0.8595 (mtp) REVERT: A 74 GLN cc_start: 0.8137 (tt0) cc_final: 0.7930 (tt0) REVERT: A 146 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7664 (mmm-85) REVERT: A 554 MET cc_start: 0.8245 (tpt) cc_final: 0.7858 (tpt) REVERT: B 146 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7662 (mmm-85) REVERT: B 290 LEU cc_start: 0.6605 (tp) cc_final: 0.5503 (pt) REVERT: B 487 PHE cc_start: 0.8047 (m-10) cc_final: 0.7696 (m-10) REVERT: C 290 LEU cc_start: 0.6584 (tp) cc_final: 0.5551 (pt) REVERT: C 487 PHE cc_start: 0.7915 (m-10) cc_final: 0.7568 (m-10) REVERT: C 554 MET cc_start: 0.8311 (tpt) cc_final: 0.7863 (tpt) REVERT: D 487 PHE cc_start: 0.7966 (m-10) cc_final: 0.7645 (m-10) REVERT: D 554 MET cc_start: 0.8337 (tpt) cc_final: 0.7889 (tpt) outliers start: 27 outliers final: 12 residues processed: 230 average time/residue: 0.5372 time to fit residues: 140.2171 Evaluate side-chains 201 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 36 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 74 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN D 369 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126191 restraints weight = 22909.756| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.71 r_work: 0.3316 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19860 Z= 0.120 Angle : 0.535 8.894 26964 Z= 0.276 Chirality : 0.039 0.133 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.304 25.054 2644 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.77 % Allowed : 15.70 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.17), residues: 2408 helix: 1.24 (0.13), residues: 1512 sheet: -2.20 (0.43), residues: 116 loop : -1.27 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 146 TYR 0.012 0.001 TYR D 555 PHE 0.012 0.001 PHE D 537 TRP 0.008 0.001 TRP A 583 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00277 (19860) covalent geometry : angle 0.53521 (26964) hydrogen bonds : bond 0.03626 ( 1086) hydrogen bonds : angle 3.85920 ( 3177) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.803 Fit side-chains REVERT: A 71 ASP cc_start: 0.6671 (t0) cc_final: 0.6423 (t0) REVERT: A 146 ARG cc_start: 0.8133 (mtp85) cc_final: 0.7668 (mmm-85) REVERT: A 487 PHE cc_start: 0.8048 (m-10) cc_final: 0.7740 (m-10) REVERT: A 528 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8757 (m) REVERT: B 487 PHE cc_start: 0.8016 (m-10) cc_final: 0.7711 (m-10) REVERT: B 528 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8761 (m) REVERT: C 290 LEU cc_start: 0.6695 (tp) cc_final: 0.5545 (pt) REVERT: C 528 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8760 (m) REVERT: C 554 MET cc_start: 0.8441 (tpt) cc_final: 0.8055 (tpt) REVERT: D 71 ASP cc_start: 0.6607 (t0) cc_final: 0.6386 (t0) REVERT: D 131 ASN cc_start: 0.8487 (m-40) cc_final: 0.8115 (m-40) REVERT: D 146 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7588 (mmm-85) REVERT: D 195 LEU cc_start: 0.7917 (mp) cc_final: 0.7677 (mt) REVERT: D 487 PHE cc_start: 0.8024 (m-10) cc_final: 0.7733 (m-10) REVERT: D 528 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8753 (m) REVERT: D 554 MET cc_start: 0.8461 (tpt) cc_final: 0.8067 (tpt) outliers start: 37 outliers final: 16 residues processed: 215 average time/residue: 0.5338 time to fit residues: 130.5016 Evaluate side-chains 209 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 238 optimal weight: 0.1980 chunk 16 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 207 optimal weight: 0.0020 chunk 126 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN B 51 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN D 214 GLN D 252 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.159499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.127604 restraints weight = 23024.423| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.72 r_work: 0.3338 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19860 Z= 0.103 Angle : 0.517 8.365 26964 Z= 0.267 Chirality : 0.038 0.126 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.246 25.786 2644 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.24 % Allowed : 15.60 % Favored : 82.16 % 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 are not related in a simple way. whole: 0.52 (0.17), residues: 2408 helix: 1.35 (0.13), residues: 1512 sheet: -2.18 (0.43), residues: 116 loop : -1.20 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 146 TYR 0.011 0.001 TYR B 555 PHE 0.010 0.001 PHE A 611 TRP 0.009 0.001 TRP A 593 HIS 0.002 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00224 (19860) covalent geometry : angle 0.51739 (26964) hydrogen bonds : bond 0.03414 ( 1086) hydrogen bonds : angle 3.82050 ( 3177) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.747 Fit side-chains REVERT: A 71 ASP cc_start: 0.6650 (t0) cc_final: 0.6434 (t0) REVERT: A 131 ASN cc_start: 0.8459 (m-40) cc_final: 0.8093 (m-40) REVERT: A 146 ARG cc_start: 0.8158 (mtp85) cc_final: 0.7698 (mmm-85) REVERT: A 487 PHE cc_start: 0.8025 (m-10) cc_final: 0.7695 (m-10) REVERT: A 554 MET cc_start: 0.8313 (tpt) cc_final: 0.7900 (tpt) REVERT: B 146 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7569 (mmm-85) REVERT: B 528 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8769 (m) REVERT: B 554 MET cc_start: 0.8361 (tpt) cc_final: 0.7918 (tpt) REVERT: C 290 LEU cc_start: 0.6653 (tp) cc_final: 0.5506 (pt) REVERT: C 487 PHE cc_start: 0.7937 (m-10) cc_final: 0.7634 (m-10) REVERT: C 528 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8761 (m) REVERT: C 554 MET cc_start: 0.8373 (tpt) cc_final: 0.7966 (tpt) REVERT: D 131 ASN cc_start: 0.8504 (m-40) cc_final: 0.8102 (m-40) REVERT: D 146 ARG cc_start: 0.8176 (mtp85) cc_final: 0.7598 (mmm-85) outliers start: 47 outliers final: 24 residues processed: 232 average time/residue: 0.5685 time to fit residues: 150.3106 Evaluate side-chains 220 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 chunk 203 optimal weight: 3.9990 chunk 80 optimal weight: 0.0170 chunk 89 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 192 optimal weight: 0.0970 chunk 191 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 201 optimal weight: 0.5980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 201 HIS A 214 GLN A 369 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 214 GLN C 261 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.160148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.128447 restraints weight = 22954.954| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.71 r_work: 0.3323 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19860 Z= 0.101 Angle : 0.519 7.100 26964 Z= 0.269 Chirality : 0.038 0.123 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.207 25.816 2644 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.05 % Allowed : 15.79 % Favored : 82.16 % 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 are not related in a simple way. whole: 0.65 (0.17), residues: 2408 helix: 1.46 (0.13), residues: 1508 sheet: -2.15 (0.43), residues: 116 loop : -1.16 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.011 0.001 TYR D 555 PHE 0.010 0.001 PHE D 537 TRP 0.009 0.001 TRP A 583 HIS 0.003 0.000 HIS C 185 Details of bonding type rmsd covalent geometry : bond 0.00218 (19860) covalent geometry : angle 0.51851 (26964) hydrogen bonds : bond 0.03340 ( 1086) hydrogen bonds : angle 3.78861 ( 3177) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 0.480 Fit side-chains REVERT: A 131 ASN cc_start: 0.8416 (m-40) cc_final: 0.8075 (m-40) REVERT: A 146 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7710 (mmm-85) REVERT: A 257 GLN cc_start: 0.7786 (pt0) cc_final: 0.7552 (mm-40) REVERT: A 487 PHE cc_start: 0.7977 (m-10) cc_final: 0.7646 (m-10) REVERT: A 554 MET cc_start: 0.8307 (tpt) cc_final: 0.7900 (tpt) REVERT: B 146 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7581 (mmm-85) REVERT: B 257 GLN cc_start: 0.7738 (pt0) cc_final: 0.7489 (mm-40) REVERT: B 487 PHE cc_start: 0.7938 (m-10) cc_final: 0.7654 (m-10) REVERT: B 554 MET cc_start: 0.8323 (tpt) cc_final: 0.7890 (tpt) REVERT: C 257 GLN cc_start: 0.7682 (pt0) cc_final: 0.7434 (mm-40) REVERT: C 487 PHE cc_start: 0.7931 (m-10) cc_final: 0.7649 (m-10) REVERT: C 528 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8772 (m) REVERT: C 554 MET cc_start: 0.8287 (tpt) cc_final: 0.7919 (tpt) REVERT: D 131 ASN cc_start: 0.8444 (m-40) cc_final: 0.8098 (m-40) REVERT: D 146 ARG cc_start: 0.8179 (mtp85) cc_final: 0.7622 (mmm-85) REVERT: D 487 PHE cc_start: 0.7907 (m-10) cc_final: 0.7638 (m-10) REVERT: D 554 MET cc_start: 0.8358 (tpt) cc_final: 0.7971 (tpt) outliers start: 43 outliers final: 21 residues processed: 237 average time/residue: 0.5429 time to fit residues: 145.9558 Evaluate side-chains 221 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 369 GLN B 51 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 261 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.158163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126211 restraints weight = 22962.025| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.71 r_work: 0.3293 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19860 Z= 0.115 Angle : 0.537 7.613 26964 Z= 0.279 Chirality : 0.039 0.158 3072 Planarity : 0.004 0.048 3416 Dihedral : 4.239 25.458 2644 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.91 % Allowed : 15.89 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.17), residues: 2408 helix: 1.43 (0.13), residues: 1512 sheet: -2.15 (0.43), residues: 116 loop : -1.12 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.011 0.001 TYR D 555 PHE 0.011 0.001 PHE A 537 TRP 0.008 0.001 TRP A 583 HIS 0.003 0.001 HIS A 157 Details of bonding type rmsd covalent geometry : bond 0.00260 (19860) covalent geometry : angle 0.53659 (26964) hydrogen bonds : bond 0.03512 ( 1086) hydrogen bonds : angle 3.83750 ( 3177) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.771 Fit side-chains REVERT: A 131 ASN cc_start: 0.8411 (m-40) cc_final: 0.8092 (m-40) REVERT: A 146 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7764 (mmm-85) REVERT: A 257 GLN cc_start: 0.7822 (pt0) cc_final: 0.7575 (mm-40) REVERT: A 487 PHE cc_start: 0.8046 (m-10) cc_final: 0.7710 (m-10) REVERT: A 554 MET cc_start: 0.8360 (tpt) cc_final: 0.7955 (tpt) REVERT: B 146 ARG cc_start: 0.8250 (mtp85) cc_final: 0.7669 (mmm-85) REVERT: B 487 PHE cc_start: 0.8039 (m-10) cc_final: 0.7738 (m-10) REVERT: B 554 MET cc_start: 0.8363 (tpt) cc_final: 0.7965 (tpt) REVERT: C 257 GLN cc_start: 0.7698 (pt0) cc_final: 0.7450 (mm-40) REVERT: C 487 PHE cc_start: 0.8018 (m-10) cc_final: 0.7730 (m-10) REVERT: C 528 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8757 (m) REVERT: C 554 MET cc_start: 0.8347 (tpt) cc_final: 0.7980 (tpt) REVERT: D 131 ASN cc_start: 0.8426 (m-40) cc_final: 0.8077 (m-40) REVERT: D 146 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7675 (mmm-85) REVERT: D 487 PHE cc_start: 0.7952 (m-10) cc_final: 0.7665 (m-10) REVERT: D 554 MET cc_start: 0.8364 (tpt) cc_final: 0.7980 (tpt) outliers start: 40 outliers final: 27 residues processed: 229 average time/residue: 0.5719 time to fit residues: 148.3874 Evaluate side-chains 223 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 195 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 229 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 214 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 261 GLN C 369 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131034 restraints weight = 22524.007| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.63 r_work: 0.3278 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19860 Z= 0.126 Angle : 0.543 8.107 26964 Z= 0.284 Chirality : 0.040 0.139 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.311 25.435 2644 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.77 % Allowed : 16.41 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2408 helix: 1.39 (0.13), residues: 1508 sheet: -2.11 (0.43), residues: 116 loop : -1.13 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.012 0.001 TYR D 555 PHE 0.011 0.001 PHE A 537 TRP 0.008 0.001 TRP B 286 HIS 0.003 0.001 HIS D 185 Details of bonding type rmsd covalent geometry : bond 0.00292 (19860) covalent geometry : angle 0.54335 (26964) hydrogen bonds : bond 0.03701 ( 1086) hydrogen bonds : angle 3.89148 ( 3177) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.771 Fit side-chains REVERT: A 131 ASN cc_start: 0.8441 (m-40) cc_final: 0.8136 (m-40) REVERT: A 146 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7887 (mmm-85) REVERT: A 195 LEU cc_start: 0.7913 (mp) cc_final: 0.7624 (mt) REVERT: B 146 ARG cc_start: 0.8398 (mtp85) cc_final: 0.7784 (mmm-85) REVERT: B 195 LEU cc_start: 0.7864 (mp) cc_final: 0.7560 (mt) REVERT: B 487 PHE cc_start: 0.8172 (m-10) cc_final: 0.7846 (m-10) REVERT: B 554 MET cc_start: 0.8355 (tpt) cc_final: 0.7944 (tpt) REVERT: C 487 PHE cc_start: 0.8159 (m-10) cc_final: 0.7845 (m-10) REVERT: C 528 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8769 (m) REVERT: C 554 MET cc_start: 0.8445 (tpt) cc_final: 0.8110 (tpt) REVERT: D 131 ASN cc_start: 0.8467 (m-40) cc_final: 0.8165 (m-40) REVERT: D 146 ARG cc_start: 0.8375 (mtp85) cc_final: 0.7777 (mmm-85) REVERT: D 252 ASN cc_start: 0.8650 (t0) cc_final: 0.8259 (t0) REVERT: D 554 MET cc_start: 0.8439 (tpt) cc_final: 0.8062 (tpt) outliers start: 37 outliers final: 25 residues processed: 215 average time/residue: 0.5829 time to fit residues: 141.3433 Evaluate side-chains 216 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 overall best weight: 0.4420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 51 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.159006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127105 restraints weight = 22960.503| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.70 r_work: 0.3329 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 19860 Z= 0.104 Angle : 0.529 8.933 26964 Z= 0.277 Chirality : 0.038 0.154 3072 Planarity : 0.004 0.048 3416 Dihedral : 4.254 25.988 2644 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.43 % Allowed : 16.79 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2408 helix: 1.44 (0.13), residues: 1504 sheet: -2.11 (0.42), residues: 116 loop : -1.08 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.011 0.001 TYR D 555 PHE 0.010 0.001 PHE D 537 TRP 0.009 0.001 TRP C 583 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00224 (19860) covalent geometry : angle 0.52871 (26964) hydrogen bonds : bond 0.03458 ( 1086) hydrogen bonds : angle 3.85509 ( 3177) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 131 ASN cc_start: 0.8361 (m-40) cc_final: 0.8078 (m-40) REVERT: A 146 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7789 (mmm-85) REVERT: A 487 PHE cc_start: 0.8053 (m-10) cc_final: 0.7729 (m-10) REVERT: A 554 MET cc_start: 0.8320 (tpt) cc_final: 0.7916 (tpt) REVERT: B 146 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7706 (mmm-85) REVERT: B 257 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7491 (mt0) REVERT: B 487 PHE cc_start: 0.8072 (m-10) cc_final: 0.7766 (m-10) REVERT: B 554 MET cc_start: 0.8260 (tpt) cc_final: 0.7883 (tpt) REVERT: C 257 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7379 (mt0) REVERT: C 487 PHE cc_start: 0.8028 (m-10) cc_final: 0.7729 (m-10) REVERT: C 528 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (m) REVERT: D 131 ASN cc_start: 0.8332 (m-40) cc_final: 0.8051 (m-40) REVERT: D 146 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7704 (mmm-85) REVERT: D 487 PHE cc_start: 0.8001 (m-10) cc_final: 0.7729 (m-10) REVERT: D 554 MET cc_start: 0.8356 (tpt) cc_final: 0.7970 (tpt) outliers start: 30 outliers final: 19 residues processed: 216 average time/residue: 0.5947 time to fit residues: 144.4041 Evaluate side-chains 214 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 20 optimal weight: 0.2980 chunk 215 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN A 214 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN B 369 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN C 261 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.159522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.127878 restraints weight = 22688.860| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.63 r_work: 0.3208 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19860 Z= 0.164 Angle : 0.588 9.383 26964 Z= 0.306 Chirality : 0.041 0.152 3072 Planarity : 0.004 0.047 3416 Dihedral : 4.453 24.889 2644 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.38 % Allowed : 17.18 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.17), residues: 2408 helix: 1.31 (0.13), residues: 1508 sheet: -1.57 (0.49), residues: 96 loop : -1.09 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.012 0.001 TYR D 555 PHE 0.012 0.001 PHE A 537 TRP 0.009 0.001 TRP C 286 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00395 (19860) covalent geometry : angle 0.58805 (26964) hydrogen bonds : bond 0.04088 ( 1086) hydrogen bonds : angle 3.99458 ( 3177) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5761.26 seconds wall clock time: 100 minutes 26.29 seconds (6026.29 seconds total)