Starting phenix.real_space_refine on Mon Jun 16 21:55:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6r_25725/06_2025/7t6r_25725.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6r_25725/06_2025/7t6r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t6r_25725/06_2025/7t6r_25725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6r_25725/06_2025/7t6r_25725.map" model { file = "/net/cci-nas-00/data/ceres_data/7t6r_25725/06_2025/7t6r_25725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6r_25725/06_2025/7t6r_25725.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.41, per 1000 atoms: 0.59 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: 5.46 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.98 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: 6.71 Time building geometry restraints manager: 6.24 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: 0.05 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.120 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.490 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.002 TRP D 583 HIS 0.010 0.001 HIS D 157 PHE 0.039 0.002 PHE C 456 TYR 0.025 0.002 TYR C 621 ARG 0.013 0.001 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.15804 ( 1086) hydrogen bonds : angle 6.72315 ( 3177) covalent geometry : bond 0.00519 (19860) covalent geometry : angle 1.07158 (26964) *********************** 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 : 2.193 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 1.3710 time to fit residues: 420.0440 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 : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.161972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.130434 restraints weight = 22954.120| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.66 r_work: 0.3381 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19860 Z= 0.126 Angle : 0.580 8.195 26964 Z= 0.302 Chirality : 0.039 0.130 3072 Planarity : 0.005 0.045 3416 Dihedral : 4.884 25.914 2644 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.91 % Allowed : 9.64 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 2408 helix: -0.17 (0.12), residues: 1508 sheet: -1.83 (0.46), residues: 96 loop : -1.71 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 583 HIS 0.003 0.001 HIS C 201 PHE 0.014 0.001 PHE D 537 TYR 0.013 0.001 TYR D 555 ARG 0.003 0.000 ARG A 43 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 1086) hydrogen bonds : angle 4.35367 ( 3177) covalent geometry : bond 0.00276 (19860) covalent geometry : angle 0.57966 (26964) *********************** 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 249 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 2.302 Fit side-chains REVERT: A 29 TRP cc_start: 0.6691 (p90) cc_final: 0.6457 (p90) REVERT: A 31 GLN cc_start: 0.7564 (pt0) cc_final: 0.7310 (pt0) REVERT: A 487 PHE cc_start: 0.7873 (m-10) cc_final: 0.7487 (m-10) REVERT: B 290 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.5489 (pt) REVERT: B 487 PHE cc_start: 0.7769 (m-10) cc_final: 0.7375 (m-10) REVERT: B 554 MET cc_start: 0.8116 (tpt) cc_final: 0.7913 (tpt) REVERT: C 290 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.5527 (pt) REVERT: C 487 PHE cc_start: 0.7765 (m-10) cc_final: 0.7371 (m-10) REVERT: D 487 PHE cc_start: 0.7807 (m-10) cc_final: 0.7470 (m-10) outliers start: 19 outliers final: 4 residues processed: 237 average time/residue: 1.4143 time to fit residues: 375.9901 Evaluate side-chains 190 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 2.390 ------------------------------------------------------------------------------- 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 25 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 211 optimal weight: 0.0770 chunk 205 optimal weight: 0.0670 chunk 152 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 overall best weight: 2.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN A 261 GLN A 369 GLN A 446 ASN B 185 HIS B 192 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 369 GLN B 446 ASN C 185 HIS ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 446 ASN 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.152662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120149 restraints weight = 22752.556| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.71 r_work: 0.3266 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19860 Z= 0.191 Angle : 0.630 8.134 26964 Z= 0.326 Chirality : 0.043 0.159 3072 Planarity : 0.005 0.045 3416 Dihedral : 4.807 25.546 2644 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.24 % Allowed : 13.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2408 helix: 0.54 (0.13), residues: 1516 sheet: -1.70 (0.48), residues: 96 loop : -1.59 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 286 HIS 0.004 0.001 HIS A 201 PHE 0.016 0.002 PHE A 537 TYR 0.014 0.002 TYR C 216 ARG 0.008 0.001 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.04612 ( 1086) hydrogen bonds : angle 4.22827 ( 3177) covalent geometry : bond 0.00464 (19860) covalent geometry : angle 0.63047 (26964) *********************** 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 248 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 2.186 Fit side-chains REVERT: A 146 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7807 (mmm-85) REVERT: A 176 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7776 (mm-30) REVERT: A 195 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7733 (mt) REVERT: B 146 ARG cc_start: 0.8271 (mtp85) cc_final: 0.7809 (mmm-85) REVERT: B 177 GLU cc_start: 0.7419 (tp30) cc_final: 0.7214 (tp30) REVERT: B 195 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7685 (mt) REVERT: D 146 ARG cc_start: 0.8285 (mtp85) cc_final: 0.7799 (mmm-85) REVERT: D 177 GLU cc_start: 0.7246 (tp30) cc_final: 0.7029 (tp30) outliers start: 47 outliers final: 15 residues processed: 228 average time/residue: 1.2741 time to fit residues: 328.8551 Evaluate side-chains 208 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 195 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 81 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain C residue 451 VAL 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 451 VAL Chi-restraints excluded: chain D residue 618 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 11 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- 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 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.155877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123766 restraints weight = 22979.148| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.71 r_work: 0.3314 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19860 Z= 0.121 Angle : 0.552 10.829 26964 Z= 0.284 Chirality : 0.040 0.138 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.560 25.589 2644 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.96 % Allowed : 14.98 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2408 helix: 0.98 (0.13), residues: 1508 sheet: -2.14 (0.44), residues: 116 loop : -1.42 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 29 HIS 0.002 0.001 HIS D 201 PHE 0.011 0.001 PHE A 537 TYR 0.015 0.001 TYR A 555 ARG 0.005 0.000 ARG D 146 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 1086) hydrogen bonds : angle 4.03077 ( 3177) covalent geometry : bond 0.00275 (19860) covalent geometry : angle 0.55226 (26964) *********************** 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 235 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 1.989 Fit side-chains REVERT: A 146 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7811 (mmm-85) REVERT: A 528 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8730 (m) REVERT: B 31 GLN cc_start: 0.7747 (pt0) cc_final: 0.7437 (pt0) REVERT: B 146 ARG cc_start: 0.8294 (mtp85) cc_final: 0.7811 (mmm-85) REVERT: B 176 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7637 (mm-30) REVERT: B 195 LEU cc_start: 0.7760 (mp) cc_final: 0.7557 (mt) REVERT: B 487 PHE cc_start: 0.8228 (m-10) cc_final: 0.7910 (m-10) REVERT: B 528 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8733 (m) REVERT: B 554 MET cc_start: 0.8390 (tpt) cc_final: 0.8077 (tpt) REVERT: B 612 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8864 (mt) REVERT: C 487 PHE cc_start: 0.8200 (m-10) cc_final: 0.7882 (m-10) REVERT: C 528 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8736 (m) REVERT: D 146 ARG cc_start: 0.8305 (mtp85) cc_final: 0.7803 (mmm-85) REVERT: D 528 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8734 (m) outliers start: 41 outliers final: 16 residues processed: 223 average time/residue: 1.2899 time to fit residues: 325.5451 Evaluate side-chains 210 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 THR 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 81 THR Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 612 LEU 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 81 THR Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 633 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 46 optimal weight: 2.9990 chunk 57 optimal weight: 0.1980 chunk 233 optimal weight: 1.9990 chunk 207 optimal weight: 0.0170 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 11 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.5020 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 214 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.158038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126160 restraints weight = 23132.369| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.72 r_work: 0.3343 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19860 Z= 0.103 Angle : 0.517 8.665 26964 Z= 0.268 Chirality : 0.038 0.128 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.355 25.429 2644 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.29 % Allowed : 15.31 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2408 helix: 1.22 (0.13), residues: 1512 sheet: -2.11 (0.44), residues: 116 loop : -1.25 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 29 HIS 0.002 0.000 HIS D 185 PHE 0.010 0.001 PHE C 537 TYR 0.013 0.001 TYR D 555 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 1086) hydrogen bonds : angle 3.88168 ( 3177) covalent geometry : bond 0.00221 (19860) covalent geometry : angle 0.51715 (26964) *********************** 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 257 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 209 time to evaluate : 2.155 Fit side-chains REVERT: A 74 GLN cc_start: 0.8154 (tt0) cc_final: 0.7722 (tt0) REVERT: A 146 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7776 (mmm-85) REVERT: A 487 PHE cc_start: 0.8170 (m-10) cc_final: 0.7855 (m-10) REVERT: A 528 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8735 (m) REVERT: A 612 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8856 (mt) REVERT: B 146 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7777 (mmm-85) REVERT: B 487 PHE cc_start: 0.8182 (m-10) cc_final: 0.7847 (m-10) REVERT: B 528 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8738 (m) REVERT: B 554 MET cc_start: 0.8295 (tpt) cc_final: 0.7991 (tpt) REVERT: C 528 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8737 (m) REVERT: D 146 ARG cc_start: 0.8256 (mtp85) cc_final: 0.7772 (mmm-85) REVERT: D 176 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7567 (mm-30) REVERT: D 487 PHE cc_start: 0.8147 (m-10) cc_final: 0.7864 (m-10) REVERT: D 528 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8739 (m) outliers start: 48 outliers final: 15 residues processed: 242 average time/residue: 1.3447 time to fit residues: 371.4929 Evaluate side-chains 216 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 612 LEU Chi-restraints excluded: chain B residue 81 THR 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 539 THR Chi-restraints excluded: chain B residue 633 VAL 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 D residue 81 THR Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 9 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125694 restraints weight = 22750.137| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.65 r_work: 0.3267 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19860 Z= 0.188 Angle : 0.601 8.112 26964 Z= 0.310 Chirality : 0.042 0.154 3072 Planarity : 0.004 0.046 3416 Dihedral : 4.569 25.056 2644 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.81 % Allowed : 15.22 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.17), residues: 2408 helix: 1.08 (0.13), residues: 1516 sheet: -1.60 (0.49), residues: 96 loop : -1.28 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 29 HIS 0.004 0.001 HIS D 122 PHE 0.013 0.001 PHE C 537 TYR 0.013 0.002 TYR C 555 ARG 0.004 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 1086) hydrogen bonds : angle 4.06659 ( 3177) covalent geometry : bond 0.00459 (19860) covalent geometry : angle 0.60064 (26964) *********************** 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 242 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 2.219 Fit side-chains REVERT: A 30 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6034 (mm-30) REVERT: A 146 ARG cc_start: 0.8497 (mtp85) cc_final: 0.8001 (mmm-85) REVERT: A 487 PHE cc_start: 0.8372 (m-10) cc_final: 0.8082 (m-10) REVERT: A 528 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8734 (m) REVERT: A 612 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8855 (mt) REVERT: B 146 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8034 (mmm-85) REVERT: B 176 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7746 (mm-30) REVERT: B 528 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8728 (m) REVERT: B 554 MET cc_start: 0.8489 (tpt) cc_final: 0.8184 (tpt) REVERT: C 487 PHE cc_start: 0.8324 (m-10) cc_final: 0.8042 (m-10) REVERT: C 528 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8727 (m) REVERT: D 146 ARG cc_start: 0.8492 (mtp85) cc_final: 0.7989 (mmm-85) REVERT: D 176 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7501 (mm-30) REVERT: D 528 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8734 (m) REVERT: D 612 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8865 (mt) outliers start: 59 outliers final: 23 residues processed: 234 average time/residue: 1.3299 time to fit residues: 356.7417 Evaluate side-chains 213 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 499 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 612 LEU Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 105 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 539 THR Chi-restraints excluded: chain B residue 633 VAL 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 81 THR Chi-restraints excluded: chain D residue 105 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 Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 612 LEU 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 171 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 232 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.154795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122882 restraints weight = 22971.547| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.71 r_work: 0.3276 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.113 Angle : 0.537 7.142 26964 Z= 0.279 Chirality : 0.039 0.133 3072 Planarity : 0.004 0.045 3416 Dihedral : 4.409 25.635 2644 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.19 % Allowed : 16.08 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.17), residues: 2408 helix: 1.18 (0.13), residues: 1524 sheet: -1.48 (0.50), residues: 96 loop : -1.24 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 593 HIS 0.003 0.001 HIS C 201 PHE 0.010 0.001 PHE A 611 TYR 0.012 0.001 TYR D 555 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 1086) hydrogen bonds : angle 3.94037 ( 3177) covalent geometry : bond 0.00250 (19860) covalent geometry : angle 0.53656 (26964) *********************** 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 244 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 198 time to evaluate : 2.355 Fit side-chains REVERT: A 30 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5861 (mm-30) REVERT: A 131 ASN cc_start: 0.8474 (m-40) cc_final: 0.8122 (m-40) REVERT: A 146 ARG cc_start: 0.8433 (mtp85) cc_final: 0.7921 (mmm-85) REVERT: A 257 GLN cc_start: 0.7833 (pt0) cc_final: 0.7591 (mm-40) REVERT: A 528 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8734 (m) REVERT: B 29 TRP cc_start: 0.6797 (p90) cc_final: 0.6559 (p90) REVERT: B 146 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7941 (mmm-85) REVERT: B 487 PHE cc_start: 0.8260 (m-10) cc_final: 0.7958 (m-10) REVERT: B 528 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8726 (m) REVERT: B 554 MET cc_start: 0.8364 (tpt) cc_final: 0.8065 (tpt) REVERT: C 257 GLN cc_start: 0.7809 (pt0) cc_final: 0.7566 (mm-40) REVERT: C 487 PHE cc_start: 0.8254 (m-10) cc_final: 0.7955 (m-10) REVERT: C 528 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8724 (m) REVERT: D 146 ARG cc_start: 0.8424 (mtp85) cc_final: 0.7914 (mmm-85) REVERT: D 176 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7465 (mm-30) REVERT: D 528 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8733 (m) outliers start: 46 outliers final: 25 residues processed: 232 average time/residue: 1.3816 time to fit residues: 365.8597 Evaluate side-chains 226 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 499 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 THR 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 105 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 539 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 520 LEU 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 105 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 Chi-restraints excluded: chain D residue 539 THR 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 80 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 0.0170 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- 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 ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129349 restraints weight = 22728.651| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.64 r_work: 0.3314 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2719 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= 0.121 Angle : 0.540 7.445 26964 Z= 0.282 Chirality : 0.039 0.137 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.376 25.124 2644 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.00 % Allowed : 16.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2408 helix: 1.25 (0.13), residues: 1524 sheet: -1.53 (0.49), residues: 96 loop : -1.16 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 583 HIS 0.003 0.001 HIS C 201 PHE 0.011 0.001 PHE C 537 TYR 0.012 0.001 TYR D 555 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1086) hydrogen bonds : angle 3.91329 ( 3177) covalent geometry : bond 0.00275 (19860) covalent geometry : angle 0.54014 (26964) *********************** 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 242 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 2.242 Fit side-chains REVERT: A 46 ASP cc_start: 0.7722 (m-30) cc_final: 0.7401 (m-30) REVERT: A 131 ASN cc_start: 0.8438 (m-40) cc_final: 0.8104 (m-40) REVERT: A 146 ARG cc_start: 0.8460 (mtp85) cc_final: 0.7960 (mmm-85) REVERT: A 257 GLN cc_start: 0.7822 (pt0) cc_final: 0.7586 (mm-40) REVERT: A 487 PHE cc_start: 0.8237 (m-10) cc_final: 0.7960 (m-10) REVERT: A 528 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8734 (m) REVERT: B 29 TRP cc_start: 0.6833 (p90) cc_final: 0.6488 (p90) REVERT: B 31 GLN cc_start: 0.7775 (pt0) cc_final: 0.7530 (pt0) REVERT: B 146 ARG cc_start: 0.8459 (mtp85) cc_final: 0.7949 (mmm-85) REVERT: B 487 PHE cc_start: 0.8253 (m-10) cc_final: 0.7962 (m-10) REVERT: B 528 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8721 (m) REVERT: B 554 MET cc_start: 0.8364 (tpt) cc_final: 0.8066 (tpt) REVERT: C 528 THR cc_start: 0.8962 (OUTLIER) cc_final: 0.8720 (m) REVERT: C 554 MET cc_start: 0.8504 (tpt) cc_final: 0.8071 (tpt) REVERT: D 131 ASN cc_start: 0.8477 (m-40) cc_final: 0.8120 (m-40) REVERT: D 146 ARG cc_start: 0.8455 (mtp85) cc_final: 0.7941 (mmm-85) REVERT: D 176 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7384 (mm-30) REVERT: D 528 THR cc_start: 0.8965 (OUTLIER) cc_final: 0.8736 (m) outliers start: 42 outliers final: 23 residues processed: 227 average time/residue: 1.3971 time to fit residues: 360.1700 Evaluate side-chains 221 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 THR 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 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 539 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR 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 148 optimal weight: 0.7980 chunk 140 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 37 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 186 optimal weight: 5.9990 chunk 228 optimal weight: 0.0070 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.155884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124028 restraints weight = 23012.464| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.71 r_work: 0.3288 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2735 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= 0.112 Angle : 0.536 8.745 26964 Z= 0.279 Chirality : 0.039 0.166 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.333 25.309 2644 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.67 % Allowed : 16.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2408 helix: 1.30 (0.13), residues: 1528 sheet: -1.51 (0.50), residues: 96 loop : -1.07 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 583 HIS 0.002 0.001 HIS C 201 PHE 0.010 0.001 PHE C 537 TYR 0.012 0.001 TYR D 555 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 1086) hydrogen bonds : angle 3.88485 ( 3177) covalent geometry : bond 0.00249 (19860) covalent geometry : angle 0.53639 (26964) *********************** 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 238 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 2.020 Fit side-chains REVERT: A 46 ASP cc_start: 0.7761 (m-30) cc_final: 0.7477 (m-30) REVERT: A 131 ASN cc_start: 0.8471 (m-40) cc_final: 0.8134 (m-40) REVERT: A 146 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7925 (mmm-85) REVERT: A 257 GLN cc_start: 0.7806 (pt0) cc_final: 0.7587 (mm-40) REVERT: A 487 PHE cc_start: 0.8251 (m-10) cc_final: 0.7936 (m-10) REVERT: A 528 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8735 (m) REVERT: A 554 MET cc_start: 0.8459 (tpt) cc_final: 0.7980 (tpt) REVERT: B 29 TRP cc_start: 0.6746 (p90) cc_final: 0.6495 (p90) REVERT: B 31 GLN cc_start: 0.7720 (pt0) cc_final: 0.7426 (pt0) REVERT: B 46 ASP cc_start: 0.7750 (m-30) cc_final: 0.7422 (m-30) REVERT: B 146 ARG cc_start: 0.8461 (mtp85) cc_final: 0.7948 (mmm-85) REVERT: B 257 GLN cc_start: 0.7802 (pt0) cc_final: 0.7558 (mm-40) REVERT: B 487 PHE cc_start: 0.8278 (m-10) cc_final: 0.7970 (m-10) REVERT: B 528 THR cc_start: 0.8947 (OUTLIER) cc_final: 0.8730 (m) REVERT: B 554 MET cc_start: 0.8337 (tpt) cc_final: 0.8043 (tpt) REVERT: C 257 GLN cc_start: 0.7789 (pt0) cc_final: 0.7571 (mm-40) REVERT: C 487 PHE cc_start: 0.8196 (m-10) cc_final: 0.7899 (m-10) REVERT: C 528 THR cc_start: 0.8957 (OUTLIER) cc_final: 0.8728 (m) REVERT: D 131 ASN cc_start: 0.8515 (m-40) cc_final: 0.8145 (m-40) REVERT: D 146 ARG cc_start: 0.8434 (mtp85) cc_final: 0.7911 (mmm-85) REVERT: D 487 PHE cc_start: 0.8193 (m-10) cc_final: 0.7923 (m-10) REVERT: D 528 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8737 (m) REVERT: D 554 MET cc_start: 0.8455 (tpt) cc_final: 0.8025 (tpt) outliers start: 35 outliers final: 20 residues processed: 228 average time/residue: 1.3091 time to fit residues: 337.0826 Evaluate side-chains 223 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 528 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 309 GLU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR 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 44 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 85 optimal weight: 0.0370 chunk 21 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.7260 ------------------------------------------------------------------------------- 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 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.155999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124237 restraints weight = 22933.298| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.71 r_work: 0.3268 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19860 Z= 0.112 Angle : 0.532 9.776 26964 Z= 0.277 Chirality : 0.039 0.136 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.306 25.241 2644 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.48 % Allowed : 16.60 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2408 helix: 1.40 (0.13), residues: 1516 sheet: -2.03 (0.44), residues: 116 loop : -0.97 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 583 HIS 0.002 0.001 HIS C 201 PHE 0.010 0.001 PHE C 537 TYR 0.012 0.001 TYR A 555 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 1086) hydrogen bonds : angle 3.86051 ( 3177) covalent geometry : bond 0.00250 (19860) covalent geometry : angle 0.53236 (26964) ********************** 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 234 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 2.353 Fit side-chains REVERT: A 46 ASP cc_start: 0.7714 (m-30) cc_final: 0.7467 (m-30) REVERT: A 131 ASN cc_start: 0.8435 (m-40) cc_final: 0.8089 (m-40) REVERT: A 146 ARG cc_start: 0.8419 (mtp85) cc_final: 0.7904 (mmm-85) REVERT: A 487 PHE cc_start: 0.8203 (m-10) cc_final: 0.7919 (m-10) REVERT: A 528 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8726 (m) REVERT: B 31 GLN cc_start: 0.7661 (pt0) cc_final: 0.7399 (pt0) REVERT: B 46 ASP cc_start: 0.7709 (m-30) cc_final: 0.7389 (m-30) REVERT: B 146 ARG cc_start: 0.8443 (mtp85) cc_final: 0.7921 (mmm-85) REVERT: B 257 GLN cc_start: 0.7769 (pt0) cc_final: 0.7529 (mm-40) REVERT: B 487 PHE cc_start: 0.8218 (m-10) cc_final: 0.7950 (m-10) REVERT: B 528 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8724 (m) REVERT: B 554 MET cc_start: 0.8340 (tpt) cc_final: 0.8066 (tpt) REVERT: C 487 PHE cc_start: 0.8191 (m-10) cc_final: 0.7926 (m-10) REVERT: C 528 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8719 (m) REVERT: C 554 MET cc_start: 0.8492 (tpt) cc_final: 0.8031 (tpt) REVERT: D 131 ASN cc_start: 0.8553 (m-40) cc_final: 0.8200 (m-40) REVERT: D 146 ARG cc_start: 0.8409 (mtp85) cc_final: 0.7896 (mmm-85) REVERT: D 487 PHE cc_start: 0.8185 (m-10) cc_final: 0.7930 (m-10) REVERT: D 528 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8729 (m) REVERT: D 554 MET cc_start: 0.8432 (tpt) cc_final: 0.8023 (tpt) outliers start: 31 outliers final: 21 residues processed: 225 average time/residue: 1.3852 time to fit residues: 357.0960 Evaluate side-chains 222 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 2.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 633 VAL 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 539 THR Chi-restraints excluded: chain B residue 633 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 528 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 539 THR 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 18 optimal weight: 3.9990 chunk 211 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 58 optimal weight: 0.0370 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** D 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.156378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124536 restraints weight = 23087.376| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.72 r_work: 0.3303 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19860 Z= 0.108 Angle : 0.532 10.285 26964 Z= 0.277 Chirality : 0.039 0.142 3072 Planarity : 0.004 0.044 3416 Dihedral : 4.290 25.319 2644 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.38 % Allowed : 16.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2408 helix: 1.38 (0.13), residues: 1512 sheet: -2.04 (0.44), residues: 116 loop : -0.97 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 29 HIS 0.002 0.001 HIS C 201 PHE 0.010 0.001 PHE C 537 TYR 0.012 0.001 TYR A 555 ARG 0.003 0.000 ARG A 146 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 1086) hydrogen bonds : angle 3.84871 ( 3177) covalent geometry : bond 0.00237 (19860) covalent geometry : angle 0.53182 (26964) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14162.61 seconds wall clock time: 248 minutes 8.18 seconds (14888.18 seconds total)