Starting phenix.real_space_refine on Fri Aug 7 22:33:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21fi_67626/08_2026/21fi_67626_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/21fi_67626/08_2026/21fi_67626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21fi_67626/08_2026/21fi_67626_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21fi_67626/08_2026/21fi_67626_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21fi_67626/08_2026/21fi_67626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21fi_67626/08_2026/21fi_67626.map" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.065 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: 6 Type Number sf(0) Gaussians S 66 5.16 5 Na 6 4.78 5 C 7824 2.51 5 N 1764 2.21 5 O 2019 1.98 5 H 11889 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23568 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 7843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 7843 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 20, 'TRANS': 481} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 13 Unusual residues: {' NA': 2, 'DQY': 1} Classifications: {'undetermined': 3, 'water': 3} Link IDs: {None: 5} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: A, B Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" C1 DQY D 601 " occ=0.69 ... (6 atoms not shown) pdb=" S DQY D 601 " occ=0.69 residue: pdb=" C1 DQY A 601 " occ=0.69 ... (6 atoms not shown) pdb=" S DQY A 601 " occ=0.69 residue: pdb=" C1 DQY B 601 " occ=0.69 ... (6 atoms not shown) pdb=" S DQY B 601 " occ=0.69 Time building chain proxies: 7.22, per 1000 atoms: 0.31 Number of scatterers: 23568 At special positions: 0 Unit cell: (111.55, 120.28, 82.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 Na 6 11.00 O 2019 8.00 N 1764 7.00 C 7824 6.00 H 11889 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 568.3 milliseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2724 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'D' and resid 8 through 28 Proline residue: D 24 - end of helix Processing helix chain 'D' and resid 28 through 68 removed outlier: 6.719A pdb=" N MET D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL D 50 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.769A pdb=" N LYS D 72 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 73 " --> pdb=" O HIS D 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 69 through 73' Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 100 through 116 removed outlier: 3.775A pdb=" N THR D 107 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N TRP D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR D 113 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 139 removed outlier: 3.675A pdb=" N ALA D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 161 removed outlier: 3.892A pdb=" N PHE D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N PHE D 148 " --> pdb=" O ALA D 144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL D 149 " --> pdb=" O TRP D 145 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 150 " --> pdb=" O ALA D 146 " (cutoff:3.500A) Proline residue: D 151 - end of helix Proline residue: D 154 - end of helix Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 173 through 178 Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 183 through 220 removed outlier: 3.804A pdb=" N LYS D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) Proline residue: D 210 - end of helix Processing helix chain 'D' and resid 225 through 247 removed outlier: 3.639A pdb=" N GLY D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 274 removed outlier: 3.700A pdb=" N LEU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 255 " --> pdb=" O GLY D 251 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 293 removed outlier: 3.503A pdb=" N GLY D 288 " --> pdb=" O THR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 299 Processing helix chain 'D' and resid 308 through 313 Processing helix chain 'D' and resid 313 through 323 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.150A pdb=" N LEU D 330 " --> pdb=" O PRO D 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE D 335 " --> pdb=" O PHE D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 373 removed outlier: 3.626A pdb=" N GLY D 352 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 359 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 370 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU D 371 " --> pdb=" O ALA D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 386 Processing helix chain 'D' and resid 386 through 396 Processing helix chain 'D' and resid 400 through 432 removed outlier: 4.081A pdb=" N THR D 419 " --> pdb=" O PHE D 415 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE D 420 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER D 422 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR D 431 " --> pdb=" O MET D 427 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 454 removed outlier: 4.396A pdb=" N PHE D 454 " --> pdb=" O ALA D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 463 removed outlier: 3.726A pdb=" N GLY D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 463 " --> pdb=" O THR D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 479 removed outlier: 3.723A pdb=" N THR D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE D 479 " --> pdb=" O ILE D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 498 removed outlier: 3.969A pdb=" N VAL D 484 " --> pdb=" O PRO D 480 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D 498 " --> pdb=" O LYS D 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 28 Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 28 through 68 removed outlier: 6.719A pdb=" N MET A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.770A pdb=" N LYS A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 73 " --> pdb=" O HIS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 73' Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.775A pdb=" N THR A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TRP A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 removed outlier: 3.675A pdb=" N ALA A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 161 removed outlier: 3.892A pdb=" N PHE A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 149 " --> pdb=" O TRP A 145 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Proline residue: A 151 - end of helix Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 182 Processing helix chain 'A' and resid 183 through 220 removed outlier: 3.804A pdb=" N LYS A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.639A pdb=" N GLY A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 274 removed outlier: 3.700A pdb=" N LEU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 293 removed outlier: 3.503A pdb=" N GLY A 288 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 324 through 335 removed outlier: 4.150A pdb=" N LEU A 330 " --> pdb=" O PRO A 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 373 removed outlier: 3.626A pdb=" N GLY A 352 " --> pdb=" O GLY A 348 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 371 " --> pdb=" O ALA A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 432 removed outlier: 4.081A pdb=" N THR A 419 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 431 " --> pdb=" O MET A 427 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 454 removed outlier: 4.396A pdb=" N PHE A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.726A pdb=" N GLY A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.723A pdb=" N THR A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 498 removed outlier: 3.969A pdb=" N VAL A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 498 " --> pdb=" O LYS A 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 28 through 68 removed outlier: 6.720A pdb=" N MET B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 73 removed outlier: 3.770A pdb=" N LYS B 72 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 73 " --> pdb=" O HIS B 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 69 through 73' Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 100 through 116 removed outlier: 3.774A pdb=" N THR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TRP B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.675A pdb=" N ALA B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 134 " --> pdb=" O GLU B 130 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 161 removed outlier: 3.892A pdb=" N PHE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 149 " --> pdb=" O TRP B 145 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 150 " --> pdb=" O ALA B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 182 Processing helix chain 'B' and resid 183 through 220 removed outlier: 3.804A pdb=" N LYS B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 225 through 247 removed outlier: 3.639A pdb=" N GLY B 247 " --> pdb=" O SER B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 274 removed outlier: 3.700A pdb=" N LEU B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 255 " --> pdb=" O GLY B 251 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 293 removed outlier: 3.503A pdb=" N GLY B 288 " --> pdb=" O THR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 313 through 323 Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.151A pdb=" N LEU B 330 " --> pdb=" O PRO B 326 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 335 " --> pdb=" O PHE B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 373 removed outlier: 3.626A pdb=" N GLY B 352 " --> pdb=" O GLY B 348 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 371 " --> pdb=" O ALA B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 386 through 396 Processing helix chain 'B' and resid 400 through 432 removed outlier: 4.081A pdb=" N THR B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 431 " --> pdb=" O MET B 427 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 454 removed outlier: 4.396A pdb=" N PHE B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.726A pdb=" N GLY B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 479 removed outlier: 3.723A pdb=" N THR B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 498 removed outlier: 3.969A pdb=" N VAL B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR B 498 " --> pdb=" O LYS B 494 " (cutoff:3.500A) 826 hydrogen bonds defined for protein. 2469 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11871 1.02 - 1.22: 84 1.22 - 1.41: 4963 1.41 - 1.61: 6854 1.61 - 1.81: 117 Bond restraints: 23889 Sorted by residual: bond pdb=" C3 DQY D 601 " pdb=" S DQY D 601 " ideal model delta sigma weight residual 1.983 1.792 0.191 2.00e-02 2.50e+03 9.16e+01 bond pdb=" C3 DQY B 601 " pdb=" S DQY B 601 " ideal model delta sigma weight residual 1.983 1.792 0.191 2.00e-02 2.50e+03 9.11e+01 bond pdb=" C3 DQY A 601 " pdb=" S DQY A 601 " ideal model delta sigma weight residual 1.983 1.792 0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" SG CYS D 95 " pdb=" HG CYS D 95 " ideal model delta sigma weight residual 1.200 1.334 -0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" SG CYS B 95 " pdb=" HG CYS B 95 " ideal model delta sigma weight residual 1.200 1.334 -0.134 2.00e-02 2.50e+03 4.52e+01 ... (remaining 23884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 43071 3.76 - 7.52: 183 7.52 - 11.27: 21 11.27 - 15.03: 0 15.03 - 18.79: 6 Bond angle restraints: 43281 Sorted by residual: angle pdb=" N GLY B 251 " pdb=" CA GLY B 251 " pdb=" C GLY B 251 " ideal model delta sigma weight residual 112.49 123.60 -11.11 1.21e+00 6.83e-01 8.43e+01 angle pdb=" N GLY D 251 " pdb=" CA GLY D 251 " pdb=" C GLY D 251 " ideal model delta sigma weight residual 112.49 123.59 -11.10 1.21e+00 6.83e-01 8.41e+01 angle pdb=" N GLY A 251 " pdb=" CA GLY A 251 " pdb=" C GLY A 251 " ideal model delta sigma weight residual 112.49 123.58 -11.09 1.21e+00 6.83e-01 8.41e+01 angle pdb=" N TYR B 104 " pdb=" CA TYR B 104 " pdb=" C TYR B 104 " ideal model delta sigma weight residual 111.14 120.02 -8.88 1.08e+00 8.57e-01 6.76e+01 angle pdb=" N TYR A 104 " pdb=" CA TYR A 104 " pdb=" C TYR A 104 " ideal model delta sigma weight residual 111.14 120.01 -8.87 1.08e+00 8.57e-01 6.75e+01 ... (remaining 43276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 10037 16.49 - 32.98: 772 32.98 - 49.47: 240 49.47 - 65.96: 195 65.96 - 82.46: 15 Dihedral angle restraints: 11259 sinusoidal: 5844 harmonic: 5415 Sorted by residual: dihedral pdb=" CA LEU D 453 " pdb=" C LEU D 453 " pdb=" N PHE D 454 " pdb=" CA PHE D 454 " ideal model delta harmonic sigma weight residual 180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LEU B 453 " pdb=" C LEU B 453 " pdb=" N PHE B 454 " pdb=" CA PHE B 454 " ideal model delta harmonic sigma weight residual -180.00 -160.88 -19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LEU A 453 " pdb=" C LEU A 453 " pdb=" N PHE A 454 " pdb=" CA PHE A 454 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 11256 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1511 0.051 - 0.102: 309 0.102 - 0.154: 64 0.154 - 0.205: 12 0.205 - 0.256: 18 Chirality restraints: 1914 Sorted by residual: chirality pdb=" CA MET B 92 " pdb=" N MET B 92 " pdb=" C MET B 92 " pdb=" CB MET B 92 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA MET A 92 " pdb=" N MET A 92 " pdb=" C MET A 92 " pdb=" CB MET A 92 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA MET D 92 " pdb=" N MET D 92 " pdb=" C MET D 92 " pdb=" CB MET D 92 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1911 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 95 " 0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C CYS B 95 " -0.061 2.00e-02 2.50e+03 pdb=" O CYS B 95 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS D 95 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C CYS D 95 " -0.061 2.00e-02 2.50e+03 pdb=" O CYS D 95 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA D 96 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 95 " 0.017 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C CYS A 95 " -0.061 2.00e-02 2.50e+03 pdb=" O CYS A 95 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 96 " 0.021 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 1453 2.22 - 2.82: 48422 2.82 - 3.41: 61245 3.41 - 4.01: 81709 4.01 - 4.60: 128817 Nonbonded interactions: 321646 Sorted by model distance: nonbonded pdb=" HH TYR D 425 " pdb=" OE2 GLU D 440 " model vdw 1.629 2.450 nonbonded pdb=" HH TYR A 425 " pdb=" OE2 GLU A 440 " model vdw 1.629 2.450 nonbonded pdb=" HH TYR B 425 " pdb=" OE2 GLU B 440 " model vdw 1.630 2.450 nonbonded pdb=" OD1 ASP A 421 " pdb=" H SER A 422 " model vdw 1.639 2.450 nonbonded pdb=" O GLY A 386 " pdb=" HG1 THR A 390 " model vdw 1.640 2.450 ... (remaining 321641 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: 0.02 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'B' } 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=0.69 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: 1.920 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: 0.150 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.007 0.191 12000 Z= 0.479 Angle : 0.928 18.789 16362 Z= 0.566 Chirality : 0.049 0.256 1914 Planarity : 0.007 0.069 1959 Dihedral : 14.386 82.456 4050 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.49 % Allowed : 11.41 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.22), residues: 1500 helix: 1.52 (0.15), residues: 1149 sheet: None (None), residues: 0 loop : -1.53 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.014 0.002 TYR B 104 PHE 0.024 0.002 PHE B 240 TRP 0.012 0.002 TRP D 110 HIS 0.005 0.002 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.48 (12000) covalent geometry : angle 0.92820 / 0.57 (16362) hydrogen bonds : bond 0.17691 / 11.51 ( 826) hydrogen bonds : angle 5.23090 / 3.73 ( 2469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.623 Fit side-chains REVERT: A 254 LEU cc_start: 0.7901 (tt) cc_final: 0.7652 (tp) REVERT: A 374 LYS cc_start: 0.8044 (mttp) cc_final: 0.7825 (mtpp) REVERT: B 78 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7443 (ttmt) REVERT: B 375 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7724 (mt-10) REVERT: B 383 GLU cc_start: 0.6849 (tp30) cc_final: 0.6647 (tp30) REVERT: B 426 MET cc_start: 0.8222 (mmm) cc_final: 0.7899 (mmp) outliers start: 6 outliers final: 5 residues processed: 158 average time/residue: 0.7298 time to fit residues: 130.2456 Evaluate side-chains 149 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.109498 restraints weight = 31873.587| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.08 r_work: 0.3080 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2989 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2989 r_free = 0.2989 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12000 Z= 0.160 Angle : 0.553 5.388 16362 Z= 0.313 Chirality : 0.038 0.146 1914 Planarity : 0.005 0.045 1959 Dihedral : 5.792 69.055 1604 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.05 % Allowed : 10.28 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1500 helix: 1.47 (0.15), residues: 1197 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 168 TYR 0.013 0.001 TYR B 300 PHE 0.023 0.002 PHE B 240 TRP 0.010 0.001 TRP A 110 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (12000) covalent geometry : angle 0.55321 / 0.31 (16362) hydrogen bonds : bond 0.08233 / 5.44 ( 826) hydrogen bonds : angle 4.31491 / 3.09 ( 2469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.545 Fit side-chains REVERT: B 375 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7641 (mt-10) REVERT: B 383 GLU cc_start: 0.6988 (tp30) cc_final: 0.6733 (tp30) REVERT: B 426 MET cc_start: 0.8400 (mmm) cc_final: 0.7961 (mmm) outliers start: 13 outliers final: 7 residues processed: 163 average time/residue: 0.6837 time to fit residues: 127.8159 Evaluate side-chains 147 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 40 ASN A 384 GLN B 384 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106856 restraints weight = 32413.696| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.12 r_work: 0.3045 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12000 Z= 0.175 Angle : 0.572 4.988 16362 Z= 0.324 Chirality : 0.039 0.154 1914 Planarity : 0.005 0.047 1959 Dihedral : 5.593 69.112 1600 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.65 % Allowed : 10.44 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.22), residues: 1500 helix: 1.51 (0.15), residues: 1182 sheet: None (None), residues: 0 loop : -1.49 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.015 0.002 TYR B 300 PHE 0.025 0.002 PHE B 240 TRP 0.013 0.002 TRP A 110 HIS 0.004 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (12000) covalent geometry : angle 0.57189 / 0.32 (16362) hydrogen bonds : bond 0.08794 / 5.82 ( 826) hydrogen bonds : angle 4.21483 / 3.01 ( 2469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 145 time to evaluate : 0.456 Fit side-chains REVERT: B 78 LYS cc_start: 0.7804 (ttmt) cc_final: 0.7515 (ttmt) REVERT: B 375 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 426 MET cc_start: 0.8561 (mmm) cc_final: 0.8187 (mmm) outliers start: 8 outliers final: 4 residues processed: 153 average time/residue: 0.7478 time to fit residues: 129.9084 Evaluate side-chains 145 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.0060 chunk 38 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 40 ASN A 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109798 restraints weight = 32552.168| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.12 r_work: 0.3092 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12000 Z= 0.147 Angle : 0.519 4.477 16362 Z= 0.293 Chirality : 0.037 0.145 1914 Planarity : 0.005 0.044 1959 Dihedral : 5.486 68.648 1600 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.81 % Allowed : 10.36 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.22), residues: 1500 helix: 1.59 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.48 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.012 0.001 TYR B 104 PHE 0.023 0.002 PHE A 240 TRP 0.010 0.001 TRP A 110 HIS 0.002 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.15 (12000) covalent geometry : angle 0.51857 / 0.29 (16362) hydrogen bonds : bond 0.07553 / 4.99 ( 826) hydrogen bonds : angle 4.11814 / 2.95 ( 2469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.595 Fit side-chains REVERT: D 18 ILE cc_start: 0.7405 (pt) cc_final: 0.7148 (pp) REVERT: A 18 ILE cc_start: 0.7284 (pt) cc_final: 0.7024 (pp) REVERT: B 78 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7478 (ttmt) REVERT: B 122 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7445 (tm-30) REVERT: B 375 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7640 (mt-10) REVERT: B 426 MET cc_start: 0.8479 (mmm) cc_final: 0.8078 (mmm) outliers start: 10 outliers final: 4 residues processed: 159 average time/residue: 0.7052 time to fit residues: 128.0074 Evaluate side-chains 147 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 40 ASN A 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.130300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104361 restraints weight = 32408.799| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.15 r_work: 0.3010 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12000 Z= 0.200 Angle : 0.616 5.779 16362 Z= 0.350 Chirality : 0.040 0.164 1914 Planarity : 0.006 0.048 1959 Dihedral : 5.648 69.392 1600 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.73 % Allowed : 10.76 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.22), residues: 1500 helix: 1.37 (0.15), residues: 1203 sheet: None (None), residues: 0 loop : -1.77 (0.33), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 296 TYR 0.015 0.002 TYR A 104 PHE 0.027 0.002 PHE B 240 TRP 0.016 0.002 TRP A 110 HIS 0.005 0.001 HIS D 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.20 (12000) covalent geometry : angle 0.61616 / 0.35 (16362) hydrogen bonds : bond 0.09573 / 6.34 ( 826) hydrogen bonds : angle 4.23472 / 3.03 ( 2469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.586 Fit side-chains REVERT: D 18 ILE cc_start: 0.7309 (pt) cc_final: 0.7058 (pp) REVERT: A 18 ILE cc_start: 0.7265 (pt) cc_final: 0.7004 (pp) REVERT: A 78 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7209 (tttp) REVERT: B 78 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7612 (ttmt) REVERT: B 375 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7715 (mt-10) REVERT: B 426 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8201 (mmm) outliers start: 9 outliers final: 6 residues processed: 145 average time/residue: 0.7660 time to fit residues: 125.8381 Evaluate side-chains 145 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 426 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN D 445 ASN A 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.105447 restraints weight = 32297.108| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.08 r_work: 0.3035 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12000 Z= 0.188 Angle : 0.591 5.211 16362 Z= 0.336 Chirality : 0.040 0.158 1914 Planarity : 0.006 0.048 1959 Dihedral : 5.643 69.475 1600 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.21 % Allowed : 10.84 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.22), residues: 1500 helix: 1.40 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.66 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.013 0.002 TYR B 300 PHE 0.024 0.002 PHE B 240 TRP 0.016 0.002 TRP A 110 HIS 0.004 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (12000) covalent geometry : angle 0.59111 / 0.34 (16362) hydrogen bonds : bond 0.09207 / 6.10 ( 826) hydrogen bonds : angle 4.23906 / 3.03 ( 2469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.618 Fit side-chains REVERT: D 18 ILE cc_start: 0.7351 (pt) cc_final: 0.7067 (pp) REVERT: D 431 THR cc_start: 0.7933 (m) cc_final: 0.7337 (p) REVERT: D 495 MET cc_start: 0.8204 (mtp) cc_final: 0.7876 (mtp) REVERT: A 18 ILE cc_start: 0.7272 (pt) cc_final: 0.7000 (pp) REVERT: A 78 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7215 (tttp) REVERT: B 78 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7631 (ttmt) REVERT: B 122 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: B 375 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 426 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8206 (mmm) REVERT: B 493 MET cc_start: 0.7188 (mmp) cc_final: 0.6784 (mtp) REVERT: B 495 MET cc_start: 0.8300 (mtm) cc_final: 0.8061 (mtm) outliers start: 15 outliers final: 9 residues processed: 151 average time/residue: 0.7068 time to fit residues: 120.4211 Evaluate side-chains 151 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain D residue 445 ASN Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 426 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 40 ASN A 384 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.107856 restraints weight = 32445.658| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.12 r_work: 0.3062 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12000 Z= 0.156 Angle : 0.540 4.582 16362 Z= 0.306 Chirality : 0.038 0.161 1914 Planarity : 0.005 0.046 1959 Dihedral : 5.551 69.232 1600 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.05 % Allowed : 11.08 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1500 helix: 1.51 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.59 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.013 0.001 TYR D 104 PHE 0.024 0.002 PHE A 240 TRP 0.019 0.001 TRP D 444 HIS 0.003 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (12000) covalent geometry : angle 0.53987 / 0.31 (16362) hydrogen bonds : bond 0.08040 / 5.32 ( 826) hydrogen bonds : angle 4.18475 / 2.99 ( 2469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.494 Fit side-chains REVERT: D 18 ILE cc_start: 0.7324 (pt) cc_final: 0.7056 (pp) REVERT: D 431 THR cc_start: 0.7876 (m) cc_final: 0.7291 (p) REVERT: A 18 ILE cc_start: 0.7270 (pt) cc_final: 0.7020 (pp) REVERT: A 78 LYS cc_start: 0.7721 (ttmt) cc_final: 0.7194 (tttp) REVERT: B 78 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7581 (ttmt) REVERT: B 122 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: B 375 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7727 (mt-10) REVERT: B 426 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8228 (mmm) outliers start: 13 outliers final: 9 residues processed: 155 average time/residue: 0.7302 time to fit residues: 128.3072 Evaluate side-chains 154 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 426 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.133098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107678 restraints weight = 32431.530| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.12 r_work: 0.3053 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12000 Z= 0.162 Angle : 0.547 5.219 16362 Z= 0.310 Chirality : 0.038 0.169 1914 Planarity : 0.005 0.045 1959 Dihedral : 5.539 69.143 1600 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.89 % Allowed : 11.33 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.22), residues: 1500 helix: 1.54 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.012 0.002 TYR D 104 PHE 0.025 0.002 PHE B 240 TRP 0.012 0.001 TRP A 110 HIS 0.003 0.001 HIS D 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (12000) covalent geometry : angle 0.54739 / 0.31 (16362) hydrogen bonds : bond 0.08161 / 5.40 ( 826) hydrogen bonds : angle 4.14732 / 2.97 ( 2469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.621 Fit side-chains REVERT: D 18 ILE cc_start: 0.7301 (pt) cc_final: 0.7042 (pp) REVERT: D 78 LYS cc_start: 0.7783 (ttmt) cc_final: 0.7111 (tttp) REVERT: D 253 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7201 (mtpt) REVERT: D 431 THR cc_start: 0.7871 (m) cc_final: 0.7280 (p) REVERT: A 18 ILE cc_start: 0.7252 (pt) cc_final: 0.7013 (pp) REVERT: A 78 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7209 (tttp) REVERT: B 78 LYS cc_start: 0.7858 (ttmt) cc_final: 0.7562 (ttmt) REVERT: B 122 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: B 426 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8189 (mmm) outliers start: 11 outliers final: 9 residues processed: 152 average time/residue: 0.7109 time to fit residues: 122.5340 Evaluate side-chains 154 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 426 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.132453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106982 restraints weight = 32428.115| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.12 r_work: 0.3049 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12000 Z= 0.170 Angle : 0.562 5.212 16362 Z= 0.318 Chirality : 0.039 0.179 1914 Planarity : 0.005 0.046 1959 Dihedral : 5.564 69.254 1600 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.21 % Allowed : 11.08 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.22), residues: 1500 helix: 1.52 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.63 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 296 TYR 0.013 0.002 TYR D 104 PHE 0.025 0.002 PHE B 240 TRP 0.013 0.002 TRP A 110 HIS 0.004 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.17 (12000) covalent geometry : angle 0.56177 / 0.32 (16362) hydrogen bonds : bond 0.08441 / 5.59 ( 826) hydrogen bonds : angle 4.16271 / 2.98 ( 2469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.468 Fit side-chains REVERT: D 18 ILE cc_start: 0.7318 (pt) cc_final: 0.7058 (pp) REVERT: D 78 LYS cc_start: 0.7830 (ttmt) cc_final: 0.7159 (tttp) REVERT: D 253 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7240 (mtpt) REVERT: D 272 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7937 (mp) REVERT: D 431 THR cc_start: 0.7900 (m) cc_final: 0.7320 (p) REVERT: A 18 ILE cc_start: 0.7267 (pt) cc_final: 0.7028 (pp) REVERT: A 78 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7201 (tttp) REVERT: B 78 LYS cc_start: 0.7865 (ttmt) cc_final: 0.7565 (ttmt) REVERT: B 122 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: B 426 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8213 (mmm) outliers start: 15 outliers final: 11 residues processed: 154 average time/residue: 0.7303 time to fit residues: 127.8369 Evaluate side-chains 156 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 426 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 140 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 149 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.134156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.108816 restraints weight = 32392.051| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.12 r_work: 0.3069 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12000 Z= 0.152 Angle : 0.530 4.849 16362 Z= 0.300 Chirality : 0.038 0.187 1914 Planarity : 0.005 0.045 1959 Dihedral : 5.502 68.994 1600 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.21 % Allowed : 11.00 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1500 helix: 1.60 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.013 0.001 TYR B 104 PHE 0.024 0.002 PHE A 240 TRP 0.011 0.001 TRP A 110 HIS 0.003 0.001 HIS B 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (12000) covalent geometry : angle 0.53023 / 0.30 (16362) hydrogen bonds : bond 0.07709 / 5.10 ( 826) hydrogen bonds : angle 4.11543 / 2.94 ( 2469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Residue THR 418 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.618 Fit side-chains REVERT: D 18 ILE cc_start: 0.7256 (pt) cc_final: 0.7003 (pp) REVERT: D 78 LYS cc_start: 0.7831 (ttmt) cc_final: 0.7160 (tttp) REVERT: D 253 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7156 (mtpt) REVERT: D 431 THR cc_start: 0.7829 (m) cc_final: 0.7254 (p) REVERT: A 18 ILE cc_start: 0.7245 (pt) cc_final: 0.7017 (pp) REVERT: A 78 LYS cc_start: 0.7760 (ttmt) cc_final: 0.7220 (tttp) REVERT: B 78 LYS cc_start: 0.7862 (ttmt) cc_final: 0.7560 (ttmt) REVERT: B 122 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: B 426 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8177 (mmm) outliers start: 15 outliers final: 12 residues processed: 158 average time/residue: 0.6840 time to fit residues: 122.7969 Evaluate side-chains 159 residues out of total 1236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 318 TRP Chi-restraints excluded: chain D residue 474 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 253 LYS Chi-restraints excluded: chain B residue 318 TRP Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 95 optimal weight: 0.3980 chunk 140 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 132 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 384 GLN A 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.108919 restraints weight = 32245.994| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.11 r_work: 0.3070 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2978 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2978 r_free = 0.2978 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2978 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12000 Z= 0.153 Angle : 0.530 4.898 16362 Z= 0.300 Chirality : 0.038 0.181 1914 Planarity : 0.005 0.045 1959 Dihedral : 5.491 68.838 1600 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.13 % Allowed : 11.08 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.22), residues: 1500 helix: 1.63 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -1.57 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 296 TYR 0.012 0.001 TYR D 104 PHE 0.024 0.002 PHE B 240 TRP 0.011 0.001 TRP A 110 HIS 0.003 0.001 HIS D 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (12000) covalent geometry : angle 0.53038 / 0.30 (16362) hydrogen bonds : bond 0.07689 / 5.09 ( 826) hydrogen bonds : angle 4.09226 / 2.92 ( 2469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6172.70 seconds wall clock time: 104 minutes 50.31 seconds (6290.31 seconds total)