Starting phenix.real_space_refine on Thu Mar 5 04:50:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t6o_25721/03_2026/7t6o_25721.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6o_25721/03_2026/7t6o_25721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t6o_25721/03_2026/7t6o_25721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6o_25721/03_2026/7t6o_25721.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t6o_25721/03_2026/7t6o_25721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6o_25721/03_2026/7t6o_25721.map" } resolution = 2.6 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 12548 2.51 5 N 3284 2.21 5 O 3440 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19412 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "C" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Chain: "D" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4853 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 24, 'TRANS': 581} Chain breaks: 1 Time building chain proxies: 4.39, per 1000 atoms: 0.23 Number of scatterers: 19412 At special positions: 0 Unit cell: (143.59, 143.59, 119.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3440 8.00 N 3284 7.00 C 12548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 901.3 milliseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 70.0% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.633A pdb=" N LEU A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.792A pdb=" N ALA A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL A 116 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.528A pdb=" N ILE A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 139 removed outlier: 3.627A pdb=" N ARG A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.506A pdb=" N GLY A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 208 through 221 removed outlier: 4.000A pdb=" N CYS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 242 through 250 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.931A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 3.932A pdb=" N SER A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 298 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG A 305 " --> pdb=" O ARG A 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 removed outlier: 3.982A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 349 Processing helix chain 'A' and resid 379 through 410 Proline residue: A 405 - end of helix removed outlier: 3.693A pdb=" N VAL A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 418 removed outlier: 3.683A pdb=" N GLN A 418 " --> pdb=" O ARG A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 445 Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 removed outlier: 4.283A pdb=" N PHE A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 512 removed outlier: 3.587A pdb=" N ARG A 492 " --> pdb=" O GLY A 488 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TRP A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 538 Processing helix chain 'A' and resid 552 through 566 removed outlier: 3.547A pdb=" N CYS A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 585 Processing helix chain 'A' and resid 585 through 608 Processing helix chain 'A' and resid 609 through 613 Processing helix chain 'A' and resid 621 through 624 removed outlier: 3.744A pdb=" N GLY A 624 " --> pdb=" O TYR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 47 through 55 Processing helix chain 'B' and resid 57 through 66 removed outlier: 3.628A pdb=" N LEU B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 Processing helix chain 'B' and resid 103 through 107 removed outlier: 3.794A pdb=" N ALA B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 removed outlier: 4.108A pdb=" N VAL B 116 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.519A pdb=" N ILE B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 139 removed outlier: 3.633A pdb=" N ARG B 139 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.504A pdb=" N GLY B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 208 through 221 removed outlier: 4.003A pdb=" N CYS B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 242 through 250 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.931A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 removed outlier: 3.912A pdb=" N SER B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 298 Processing helix chain 'B' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG B 305 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 324 removed outlier: 3.983A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 349 Processing helix chain 'B' and resid 379 through 410 Proline residue: B 405 - end of helix removed outlier: 3.694A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 418 removed outlier: 3.684A pdb=" N GLN B 418 " --> pdb=" O ARG B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 445 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 487 removed outlier: 4.283A pdb=" N PHE B 478 " --> pdb=" O MET B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 512 removed outlier: 3.592A pdb=" N ARG B 492 " --> pdb=" O GLY B 488 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP B 495 " --> pdb=" O MET B 491 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 496 " --> pdb=" O ARG B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 538 Processing helix chain 'B' and resid 552 through 566 removed outlier: 3.548A pdb=" N CYS B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 585 Processing helix chain 'B' and resid 585 through 608 Processing helix chain 'B' and resid 609 through 613 Processing helix chain 'B' and resid 621 through 624 removed outlier: 3.747A pdb=" N GLY B 624 " --> pdb=" O TYR B 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 621 through 624' Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.628A pdb=" N LEU C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.790A pdb=" N ALA C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL C 116 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.529A pdb=" N ILE C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 139 removed outlier: 3.630A pdb=" N ARG C 139 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 174 removed outlier: 3.519A pdb=" N GLY C 174 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.999A pdb=" N CYS C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 242 through 250 Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.923A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.906A pdb=" N SER C 285 " --> pdb=" O THR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 298 Processing helix chain 'C' and resid 302 through 309 removed outlier: 3.847A pdb=" N ARG C 305 " --> pdb=" O ARG C 302 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 324 removed outlier: 4.005A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 349 Processing helix chain 'C' and resid 379 through 410 Proline residue: C 405 - end of helix removed outlier: 3.693A pdb=" N VAL C 410 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 418 removed outlier: 3.684A pdb=" N GLN C 418 " --> pdb=" O ARG C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 445 Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.608A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 487 removed outlier: 4.278A pdb=" N PHE C 478 " --> pdb=" O MET C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 512 removed outlier: 3.608A pdb=" N ARG C 492 " --> pdb=" O GLY C 488 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TRP C 495 " --> pdb=" O MET C 491 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 496 " --> pdb=" O ARG C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 538 Processing helix chain 'C' and resid 552 through 566 removed outlier: 3.599A pdb=" N CYS C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 585 Processing helix chain 'C' and resid 585 through 608 Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 621 through 624 removed outlier: 3.759A pdb=" N GLY C 624 " --> pdb=" O TYR C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 57 through 66 removed outlier: 3.633A pdb=" N LEU D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 Processing helix chain 'D' and resid 103 through 107 removed outlier: 3.793A pdb=" N ALA D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 116 removed outlier: 4.106A pdb=" N VAL D 116 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.528A pdb=" N ILE D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 139 removed outlier: 3.629A pdb=" N ARG D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 removed outlier: 3.506A pdb=" N GLY D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 removed outlier: 4.000A pdb=" N CYS D 213 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 242 through 250 Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.927A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.941A pdb=" N SER D 285 " --> pdb=" O THR D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 298 Processing helix chain 'D' and resid 302 through 309 removed outlier: 3.846A pdb=" N ARG D 305 " --> pdb=" O ARG D 302 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 324 removed outlier: 3.985A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 349 Processing helix chain 'D' and resid 379 through 410 Proline residue: D 405 - end of helix removed outlier: 3.693A pdb=" N VAL D 410 " --> pdb=" O ASP D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 418 removed outlier: 3.683A pdb=" N GLN D 418 " --> pdb=" O ARG D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 445 Processing helix chain 'D' and resid 450 through 464 Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.609A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 487 removed outlier: 4.284A pdb=" N PHE D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 512 removed outlier: 3.618A pdb=" N ARG D 492 " --> pdb=" O GLY D 488 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 495 " --> pdb=" O MET D 491 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU D 496 " --> pdb=" O ARG D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 538 Processing helix chain 'D' and resid 552 through 566 removed outlier: 3.546A pdb=" N CYS D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 585 Processing helix chain 'D' and resid 585 through 608 Processing helix chain 'D' and resid 609 through 613 Processing helix chain 'D' and resid 621 through 624 removed outlier: 3.740A pdb=" N GLY D 624 " --> pdb=" O TYR D 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 621 through 624' Processing sheet with id=AA1, first strand: chain 'A' and resid 264 through 270 removed outlier: 6.706A pdb=" N SER A 275 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR A 269 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 354 Processing sheet with id=AA3, first strand: chain 'B' and resid 264 through 270 removed outlier: 6.706A pdb=" N SER B 275 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR B 269 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 352 through 354 Processing sheet with id=AA5, first strand: chain 'C' and resid 264 through 270 removed outlier: 6.697A pdb=" N SER C 275 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 269 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 264 through 270 removed outlier: 6.703A pdb=" N SER D 275 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR D 269 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 352 through 354 1129 hydrogen bonds defined for protein. 3219 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6195 1.34 - 1.46: 4253 1.46 - 1.58: 9184 1.58 - 1.70: 0 1.70 - 1.82: 228 Bond restraints: 19860 Sorted by residual: bond pdb=" C THR A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.85e+00 bond pdb=" C THR B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.337 1.367 -0.030 1.24e-02 6.50e+03 5.81e+00 bond pdb=" C THR C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.337 1.367 -0.029 1.24e-02 6.50e+03 5.62e+00 bond pdb=" C THR D 311 " pdb=" N PRO D 312 " ideal model delta sigma weight residual 1.337 1.366 -0.029 1.24e-02 6.50e+03 5.38e+00 bond pdb=" C VAL B 452 " pdb=" N PRO B 453 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.38e+00 ... (remaining 19855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 25931 1.77 - 3.53: 828 3.53 - 5.30: 124 5.30 - 7.07: 64 7.07 - 8.83: 17 Bond angle restraints: 26964 Sorted by residual: angle pdb=" N GLU C 591 " pdb=" CA GLU C 591 " pdb=" CB GLU C 591 " ideal model delta sigma weight residual 110.28 117.34 -7.06 1.55e+00 4.16e-01 2.07e+01 angle pdb=" N GLU A 591 " pdb=" CA GLU A 591 " pdb=" CB GLU A 591 " ideal model delta sigma weight residual 110.28 117.31 -7.03 1.55e+00 4.16e-01 2.06e+01 angle pdb=" N GLU D 591 " pdb=" CA GLU D 591 " pdb=" CB GLU D 591 " ideal model delta sigma weight residual 110.28 117.28 -7.00 1.55e+00 4.16e-01 2.04e+01 angle pdb=" N GLU B 591 " pdb=" CA GLU B 591 " pdb=" CB GLU B 591 " ideal model delta sigma weight residual 110.28 117.28 -7.00 1.55e+00 4.16e-01 2.04e+01 angle pdb=" CA GLU B 591 " pdb=" CB GLU B 591 " pdb=" CG GLU B 591 " ideal model delta sigma weight residual 114.10 121.29 -7.19 2.00e+00 2.50e-01 1.29e+01 ... (remaining 26959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 10669 17.04 - 34.07: 903 34.07 - 51.11: 168 51.11 - 68.15: 44 68.15 - 85.18: 28 Dihedral angle restraints: 11812 sinusoidal: 4732 harmonic: 7080 Sorted by residual: dihedral pdb=" CA MET C 474 " pdb=" C MET C 474 " pdb=" N LEU C 475 " pdb=" CA LEU C 475 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA MET B 474 " pdb=" C MET B 474 " pdb=" N LEU B 475 " pdb=" CA LEU B 475 " ideal model delta harmonic sigma weight residual -180.00 -163.77 -16.23 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA MET A 474 " pdb=" C MET A 474 " pdb=" N LEU A 475 " pdb=" CA LEU A 475 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2716 0.074 - 0.148: 333 0.148 - 0.223: 19 0.223 - 0.297: 0 0.297 - 0.371: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CB VAL D 297 " pdb=" CA VAL D 297 " pdb=" CG1 VAL D 297 " pdb=" CG2 VAL D 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL A 297 " pdb=" CA VAL A 297 " pdb=" CG1 VAL A 297 " pdb=" CG2 VAL A 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL B 297 " pdb=" CA VAL B 297 " pdb=" CG1 VAL B 297 " pdb=" CG2 VAL B 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 3069 not shown) Planarity restraints: 3416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 476 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 477 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 477 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 477 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 476 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 477 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 477 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 477 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 476 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO C 477 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 477 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 477 " 0.030 5.00e-02 4.00e+02 ... (remaining 3413 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5632 2.82 - 3.34: 18026 3.34 - 3.86: 34068 3.86 - 4.38: 40083 4.38 - 4.90: 67034 Nonbonded interactions: 164843 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.303 3.040 nonbonded pdb=" O PRO B 544 " pdb=" OH TYR B 555 " model vdw 2.342 3.040 ... (remaining 164838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.990 Find NCS groups from input model: 0.160 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:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 : 0.004 0.057 19860 Z= 0.211 Angle : 0.793 8.831 26964 Z= 0.430 Chirality : 0.048 0.371 3072 Planarity : 0.007 0.065 3416 Dihedral : 14.057 85.182 7236 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.15), residues: 2408 helix: -0.80 (0.11), residues: 1484 sheet: -1.14 (0.45), residues: 128 loop : -1.16 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 35 TYR 0.013 0.002 TYR A 623 PHE 0.022 0.002 PHE B 553 TRP 0.021 0.002 TRP B 593 HIS 0.005 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00427 (19860) covalent geometry : angle 0.79305 (26964) hydrogen bonds : bond 0.13914 ( 1129) hydrogen bonds : angle 5.37764 ( 3219) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.733 Fit side-chains REVERT: A 233 GLU cc_start: 0.7625 (tt0) cc_final: 0.6999 (mm-30) REVERT: B 139 ARG cc_start: 0.7122 (mtp180) cc_final: 0.6908 (mmm160) REVERT: B 233 GLU cc_start: 0.7624 (tt0) cc_final: 0.6993 (mm-30) REVERT: C 139 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6903 (mmm160) REVERT: C 233 GLU cc_start: 0.7638 (tt0) cc_final: 0.7003 (mm-30) REVERT: D 233 GLU cc_start: 0.7623 (tt0) cc_final: 0.6997 (mm-30) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.6747 time to fit residues: 278.9649 Evaluate side-chains 310 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 0.2980 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 208 ASN A 587 GLN B 131 ASN B 208 ASN B 587 GLN C 131 ASN C 208 ASN C 587 GLN D 131 ASN D 208 ASN D 587 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.178642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147739 restraints weight = 19776.404| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.22 r_work: 0.3438 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19860 Z= 0.135 Angle : 0.504 5.905 26964 Z= 0.267 Chirality : 0.039 0.128 3072 Planarity : 0.005 0.042 3416 Dihedral : 4.128 15.828 2644 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Rotamer: Outliers : 2.53 % Allowed : 6.68 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2408 helix: 0.75 (0.13), residues: 1496 sheet: -1.21 (0.45), residues: 128 loop : -0.57 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 302 TYR 0.013 0.002 TYR D 555 PHE 0.019 0.002 PHE C 537 TRP 0.015 0.001 TRP C 593 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00302 (19860) covalent geometry : angle 0.50414 (26964) hydrogen bonds : bond 0.04454 ( 1129) hydrogen bonds : angle 3.87820 ( 3219) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 317 time to evaluate : 0.614 Fit side-chains REVERT: A 38 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7349 (ttm) REVERT: A 289 GLU cc_start: 0.6970 (pm20) cc_final: 0.6417 (mm-30) REVERT: A 302 ARG cc_start: 0.7291 (ttt-90) cc_final: 0.7075 (ttt90) REVERT: A 491 MET cc_start: 0.8471 (tpp) cc_final: 0.8143 (tpt) REVERT: A 589 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7220 (ttm170) REVERT: B 38 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7365 (ttm) REVERT: B 129 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7570 (m-40) REVERT: B 139 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7060 (mmm160) REVERT: B 289 GLU cc_start: 0.6865 (pm20) cc_final: 0.6366 (mm-30) REVERT: B 302 ARG cc_start: 0.7242 (ttt-90) cc_final: 0.7022 (ttt90) REVERT: B 491 MET cc_start: 0.8451 (tpp) cc_final: 0.8150 (tpt) REVERT: B 589 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7220 (ttm170) REVERT: C 38 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7389 (ttm) REVERT: C 139 ARG cc_start: 0.7413 (mtp180) cc_final: 0.7079 (mmm160) REVERT: C 302 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.7073 (ttt90) REVERT: C 589 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7218 (ttm170) REVERT: D 38 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7386 (ttm) REVERT: D 302 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.7047 (ttt90) REVERT: D 491 MET cc_start: 0.8448 (tpp) cc_final: 0.8147 (tpt) REVERT: D 589 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7209 (ttm170) outliers start: 53 outliers final: 1 residues processed: 350 average time/residue: 0.6529 time to fit residues: 256.4314 Evaluate side-chains 322 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 316 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 228 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 119 optimal weight: 0.3980 chunk 145 optimal weight: 0.0050 overall best weight: 1.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.176483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144823 restraints weight = 19739.793| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.11 r_work: 0.3403 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19860 Z= 0.157 Angle : 0.516 5.946 26964 Z= 0.272 Chirality : 0.040 0.136 3072 Planarity : 0.004 0.039 3416 Dihedral : 4.116 15.898 2644 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.24 % Allowed : 9.88 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.17), residues: 2408 helix: 1.25 (0.13), residues: 1500 sheet: -1.20 (0.45), residues: 128 loop : -0.37 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 302 TYR 0.013 0.002 TYR B 555 PHE 0.016 0.002 PHE C 537 TRP 0.017 0.001 TRP D 593 HIS 0.004 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00367 (19860) covalent geometry : angle 0.51626 (26964) hydrogen bonds : bond 0.04635 ( 1129) hydrogen bonds : angle 3.75740 ( 3219) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 317 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ARG cc_start: 0.7482 (tpt90) cc_final: 0.6996 (mmm160) REVERT: A 326 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7727 (ttm110) REVERT: A 491 MET cc_start: 0.8549 (tpp) cc_final: 0.8249 (tpt) REVERT: B 35 ARG cc_start: 0.7485 (tpt90) cc_final: 0.7027 (mmm160) REVERT: B 38 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7512 (mtm) REVERT: B 129 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7779 (m-40) REVERT: B 139 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7086 (mmm160) REVERT: B 289 GLU cc_start: 0.6940 (pm20) cc_final: 0.6497 (mm-30) REVERT: B 326 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7711 (ttm110) REVERT: C 35 ARG cc_start: 0.7507 (tpt90) cc_final: 0.7038 (mmm160) REVERT: C 38 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7540 (mtm) REVERT: C 139 ARG cc_start: 0.7518 (mtp180) cc_final: 0.7102 (mmm160) REVERT: C 326 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7710 (ttm110) REVERT: C 578 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8396 (mtm) REVERT: D 35 ARG cc_start: 0.7500 (tpt90) cc_final: 0.7022 (mmm160) REVERT: D 38 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7549 (mtm) REVERT: D 326 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7720 (ttm110) REVERT: D 491 MET cc_start: 0.8513 (tpp) cc_final: 0.8216 (tpt) outliers start: 47 outliers final: 17 residues processed: 342 average time/residue: 0.7211 time to fit residues: 274.2138 Evaluate side-chains 335 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 38 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 226 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 158 optimal weight: 6.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.178509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.146651 restraints weight = 19660.813| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.10 r_work: 0.3433 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19860 Z= 0.120 Angle : 0.474 5.834 26964 Z= 0.249 Chirality : 0.039 0.126 3072 Planarity : 0.004 0.055 3416 Dihedral : 3.888 14.738 2644 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.86 % Allowed : 11.07 % Favored : 87.07 % 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: 1.21 (0.17), residues: 2408 helix: 1.53 (0.13), residues: 1508 sheet: -1.11 (0.45), residues: 128 loop : -0.19 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 302 TYR 0.013 0.001 TYR B 555 PHE 0.011 0.001 PHE C 537 TRP 0.016 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00269 (19860) covalent geometry : angle 0.47430 (26964) hydrogen bonds : bond 0.04134 ( 1129) hydrogen bonds : angle 3.62657 ( 3219) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 324 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7700 (ttm110) REVERT: A 491 MET cc_start: 0.8440 (tpp) cc_final: 0.8180 (tpt) REVERT: A 578 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8369 (mtm) REVERT: B 35 ARG cc_start: 0.7443 (tpt90) cc_final: 0.6546 (mtt90) REVERT: B 129 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: B 139 ARG cc_start: 0.7509 (mtp180) cc_final: 0.7074 (mmm160) REVERT: B 289 GLU cc_start: 0.6926 (pm20) cc_final: 0.6629 (mm-30) REVERT: B 326 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7697 (ttm110) REVERT: B 491 MET cc_start: 0.8386 (tpp) cc_final: 0.8004 (tpt) REVERT: C 139 ARG cc_start: 0.7502 (mtp180) cc_final: 0.7072 (mmm160) REVERT: C 326 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7695 (ttm110) REVERT: C 578 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8390 (mtm) REVERT: D 326 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7694 (ttm110) REVERT: D 491 MET cc_start: 0.8420 (tpp) cc_final: 0.8161 (tpt) outliers start: 39 outliers final: 17 residues processed: 345 average time/residue: 0.6919 time to fit residues: 266.2187 Evaluate side-chains 321 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 297 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 326 ARG Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 76 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 chunk 168 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN B 587 GLN C 131 ASN D 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.178742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147220 restraints weight = 19595.093| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.96 r_work: 0.3435 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19860 Z= 0.112 Angle : 0.467 5.801 26964 Z= 0.244 Chirality : 0.038 0.123 3072 Planarity : 0.004 0.042 3416 Dihedral : 3.762 14.205 2644 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.62 % Allowed : 12.79 % Favored : 85.59 % 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: 1.43 (0.17), residues: 2408 helix: 1.76 (0.13), residues: 1500 sheet: -1.09 (0.45), residues: 128 loop : -0.22 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 302 TYR 0.012 0.001 TYR A 555 PHE 0.010 0.001 PHE C 534 TRP 0.015 0.001 TRP B 593 HIS 0.003 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00249 (19860) covalent geometry : angle 0.46723 (26964) hydrogen bonds : bond 0.04002 ( 1129) hydrogen bonds : angle 3.56590 ( 3219) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 306 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7881 (tt0) cc_final: 0.6987 (mm-30) REVERT: A 326 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7704 (ttm110) REVERT: A 381 GLN cc_start: 0.5435 (tp40) cc_final: 0.4694 (mp10) REVERT: A 491 MET cc_start: 0.8489 (tpp) cc_final: 0.8233 (tpt) REVERT: A 578 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (mtm) REVERT: B 129 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7746 (m-40) REVERT: B 139 ARG cc_start: 0.7510 (mtp180) cc_final: 0.7051 (mmm160) REVERT: B 233 GLU cc_start: 0.7866 (tt0) cc_final: 0.6989 (mm-30) REVERT: B 289 GLU cc_start: 0.6941 (pm20) cc_final: 0.6566 (mm-30) REVERT: B 491 MET cc_start: 0.8368 (tpp) cc_final: 0.8062 (tpt) REVERT: C 139 ARG cc_start: 0.7478 (mtp180) cc_final: 0.7024 (mmm160) REVERT: C 233 GLU cc_start: 0.7854 (tt0) cc_final: 0.6989 (mm-30) REVERT: C 578 MET cc_start: 0.8600 (ttm) cc_final: 0.8400 (mtm) REVERT: D 233 GLU cc_start: 0.7866 (tt0) cc_final: 0.7004 (mm-30) REVERT: D 326 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7706 (ttm110) REVERT: D 381 GLN cc_start: 0.5438 (tp40) cc_final: 0.4710 (mp10) REVERT: D 491 MET cc_start: 0.8463 (tpp) cc_final: 0.8206 (tpt) outliers start: 34 outliers final: 22 residues processed: 329 average time/residue: 0.6565 time to fit residues: 241.7527 Evaluate side-chains 329 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 303 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 238 optimal weight: 0.9980 chunk 16 optimal weight: 0.0000 chunk 68 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.178894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147417 restraints weight = 19645.273| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.92 r_work: 0.3433 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19860 Z= 0.113 Angle : 0.468 5.787 26964 Z= 0.243 Chirality : 0.038 0.123 3072 Planarity : 0.004 0.042 3416 Dihedral : 3.713 13.964 2644 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.00 % Allowed : 12.74 % Favored : 85.26 % 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: 1.53 (0.17), residues: 2408 helix: 1.82 (0.13), residues: 1508 sheet: -1.43 (0.43), residues: 136 loop : -0.03 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 302 TYR 0.013 0.001 TYR B 555 PHE 0.010 0.001 PHE C 534 TRP 0.014 0.001 TRP C 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00251 (19860) covalent geometry : angle 0.46772 (26964) hydrogen bonds : bond 0.03979 ( 1129) hydrogen bonds : angle 3.54288 ( 3219) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7894 (tt0) cc_final: 0.7007 (mm-30) REVERT: A 326 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7738 (ttm110) REVERT: A 381 GLN cc_start: 0.5506 (tp40) cc_final: 0.4747 (mp10) REVERT: A 491 MET cc_start: 0.8553 (tpp) cc_final: 0.8309 (tpt) REVERT: A 578 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8392 (mtm) REVERT: A 591 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7826 (mt-10) REVERT: B 129 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7726 (m-40) REVERT: B 139 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7036 (mmm160) REVERT: B 233 GLU cc_start: 0.7867 (tt0) cc_final: 0.6986 (mm-30) REVERT: B 289 GLU cc_start: 0.6976 (pm20) cc_final: 0.6629 (mm-30) REVERT: B 381 GLN cc_start: 0.5522 (tp40) cc_final: 0.4715 (mp10) REVERT: B 491 MET cc_start: 0.8402 (tpp) cc_final: 0.8101 (tpt) REVERT: C 139 ARG cc_start: 0.7493 (mtp180) cc_final: 0.7025 (mmm160) REVERT: C 233 GLU cc_start: 0.7871 (tt0) cc_final: 0.6994 (mm-30) REVERT: C 381 GLN cc_start: 0.5524 (tp40) cc_final: 0.4712 (mp10) REVERT: C 485 MET cc_start: 0.7904 (mmt) cc_final: 0.7685 (mmt) REVERT: D 233 GLU cc_start: 0.7884 (tt0) cc_final: 0.7016 (mm-30) REVERT: D 381 GLN cc_start: 0.5510 (tp40) cc_final: 0.4761 (mp10) REVERT: D 491 MET cc_start: 0.8491 (tpp) cc_final: 0.8267 (tpt) outliers start: 42 outliers final: 24 residues processed: 329 average time/residue: 0.6848 time to fit residues: 252.7419 Evaluate side-chains 327 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 190 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 234 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.175284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.143265 restraints weight = 19543.099| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.00 r_work: 0.3392 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19860 Z= 0.180 Angle : 0.543 5.922 26964 Z= 0.284 Chirality : 0.042 0.140 3072 Planarity : 0.004 0.043 3416 Dihedral : 4.056 15.568 2644 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.72 % Allowed : 13.22 % Favored : 85.07 % 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 (0.17), residues: 2408 helix: 1.61 (0.13), residues: 1500 sheet: -1.06 (0.47), residues: 128 loop : -0.14 (0.24), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 302 TYR 0.014 0.002 TYR C 555 PHE 0.013 0.002 PHE A 472 TRP 0.016 0.002 TRP B 593 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00430 (19860) covalent geometry : angle 0.54294 (26964) hydrogen bonds : bond 0.04739 ( 1129) hydrogen bonds : angle 3.71835 ( 3219) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 314 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7698 (ttm110) REVERT: A 381 GLN cc_start: 0.5514 (tp40) cc_final: 0.5148 (mm-40) REVERT: A 491 MET cc_start: 0.8637 (tpp) cc_final: 0.8405 (tpt) REVERT: A 578 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8396 (mtm) REVERT: B 129 ASN cc_start: 0.8418 (OUTLIER) cc_final: 0.7920 (m-40) REVERT: B 139 ARG cc_start: 0.7608 (mtp180) cc_final: 0.7270 (mmt-90) REVERT: B 289 GLU cc_start: 0.7003 (pm20) cc_final: 0.6625 (mm-30) REVERT: B 381 GLN cc_start: 0.5588 (tp40) cc_final: 0.5163 (mm-40) REVERT: B 491 MET cc_start: 0.8487 (tpp) cc_final: 0.8204 (tpt) REVERT: C 139 ARG cc_start: 0.7597 (mtp180) cc_final: 0.7257 (mmt-90) REVERT: C 381 GLN cc_start: 0.5621 (tp40) cc_final: 0.5187 (mm-40) REVERT: D 326 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7715 (ttm110) REVERT: D 381 GLN cc_start: 0.5549 (tp40) cc_final: 0.5178 (mm-40) REVERT: D 491 MET cc_start: 0.8579 (tpp) cc_final: 0.8330 (tpt) outliers start: 36 outliers final: 21 residues processed: 340 average time/residue: 0.6518 time to fit residues: 248.5625 Evaluate side-chains 331 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 306 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 220 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 159 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN B 587 GLN C 131 ASN C 587 GLN D 131 ASN D 587 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.177659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145660 restraints weight = 19620.916| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.97 r_work: 0.3414 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.123 Angle : 0.495 6.176 26964 Z= 0.258 Chirality : 0.039 0.127 3072 Planarity : 0.004 0.052 3416 Dihedral : 3.849 14.411 2644 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.72 % Allowed : 13.55 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.48 (0.17), residues: 2408 helix: 1.77 (0.13), residues: 1500 sheet: -1.32 (0.45), residues: 136 loop : -0.04 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 302 TYR 0.013 0.001 TYR D 555 PHE 0.012 0.001 PHE C 553 TRP 0.016 0.001 TRP C 593 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00278 (19860) covalent geometry : angle 0.49522 (26964) hydrogen bonds : bond 0.04190 ( 1129) hydrogen bonds : angle 3.62534 ( 3219) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7886 (tt0) cc_final: 0.7024 (mm-30) REVERT: A 326 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7743 (ttm110) REVERT: A 381 GLN cc_start: 0.5492 (tp40) cc_final: 0.5122 (mm-40) REVERT: A 491 MET cc_start: 0.8572 (tpp) cc_final: 0.8336 (tpt) REVERT: A 591 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 129 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.7876 (m-40) REVERT: B 139 ARG cc_start: 0.7543 (mtp180) cc_final: 0.7202 (mmt-90) REVERT: B 233 GLU cc_start: 0.7853 (tt0) cc_final: 0.6987 (mm-30) REVERT: B 289 GLU cc_start: 0.7014 (pm20) cc_final: 0.6613 (mm-30) REVERT: B 381 GLN cc_start: 0.5552 (tp40) cc_final: 0.5149 (mm-40) REVERT: B 491 MET cc_start: 0.8480 (tpp) cc_final: 0.8225 (tpt) REVERT: C 139 ARG cc_start: 0.7501 (mtp180) cc_final: 0.7162 (mmt-90) REVERT: C 233 GLU cc_start: 0.7876 (tt0) cc_final: 0.7010 (mm-30) REVERT: C 381 GLN cc_start: 0.5568 (tp40) cc_final: 0.5163 (mm-40) REVERT: D 233 GLU cc_start: 0.7875 (tt0) cc_final: 0.7010 (mm-30) REVERT: D 326 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7726 (ttm110) REVERT: D 381 GLN cc_start: 0.5499 (tp40) cc_final: 0.5127 (mm-40) REVERT: D 491 MET cc_start: 0.8503 (tpp) cc_final: 0.8247 (tpt) outliers start: 36 outliers final: 25 residues processed: 329 average time/residue: 0.6789 time to fit residues: 250.1988 Evaluate side-chains 334 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 306 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 129 ASN Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 195 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 209 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 229 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN C 131 ASN D 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145953 restraints weight = 19544.628| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.92 r_work: 0.3429 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19860 Z= 0.122 Angle : 0.501 7.733 26964 Z= 0.259 Chirality : 0.039 0.127 3072 Planarity : 0.004 0.055 3416 Dihedral : 3.800 14.305 2644 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 1.34 % Allowed : 14.50 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.17), residues: 2408 helix: 1.80 (0.13), residues: 1508 sheet: -1.37 (0.44), residues: 136 loop : 0.06 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 302 TYR 0.013 0.001 TYR D 555 PHE 0.010 0.001 PHE C 534 TRP 0.015 0.001 TRP C 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00276 (19860) covalent geometry : angle 0.50089 (26964) hydrogen bonds : bond 0.04132 ( 1129) hydrogen bonds : angle 3.58760 ( 3219) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 308 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7869 (tt0) cc_final: 0.7030 (mm-30) REVERT: A 326 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7735 (ttm110) REVERT: A 381 GLN cc_start: 0.5475 (tp40) cc_final: 0.5101 (mm-40) REVERT: A 491 MET cc_start: 0.8571 (tpp) cc_final: 0.8341 (tpt) REVERT: A 591 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 139 ARG cc_start: 0.7558 (mtp180) cc_final: 0.7210 (mmt-90) REVERT: B 233 GLU cc_start: 0.7842 (tt0) cc_final: 0.6991 (mm-30) REVERT: B 289 GLU cc_start: 0.7059 (pm20) cc_final: 0.6669 (mm-30) REVERT: B 381 GLN cc_start: 0.5540 (tp40) cc_final: 0.5131 (mm-40) REVERT: B 491 MET cc_start: 0.8501 (tpp) cc_final: 0.8236 (tpt) REVERT: C 139 ARG cc_start: 0.7512 (mtp180) cc_final: 0.7166 (mmt-90) REVERT: C 233 GLU cc_start: 0.7863 (tt0) cc_final: 0.7018 (mm-30) REVERT: C 289 GLU cc_start: 0.7177 (pm20) cc_final: 0.6379 (tm-30) REVERT: C 381 GLN cc_start: 0.5556 (tp40) cc_final: 0.5146 (mm-40) REVERT: D 233 GLU cc_start: 0.7862 (tt0) cc_final: 0.7007 (mm-30) REVERT: D 326 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7744 (ttm110) REVERT: D 381 GLN cc_start: 0.5506 (tp40) cc_final: 0.5117 (mm-40) REVERT: D 491 MET cc_start: 0.8485 (tpp) cc_final: 0.8225 (tpt) outliers start: 28 outliers final: 25 residues processed: 328 average time/residue: 0.6585 time to fit residues: 242.5172 Evaluate side-chains 328 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 301 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 165 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN B 587 GLN C 131 ASN C 587 GLN D 131 ASN D 587 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.146047 restraints weight = 19612.188| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.95 r_work: 0.3424 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.123 Angle : 0.509 8.909 26964 Z= 0.262 Chirality : 0.039 0.127 3072 Planarity : 0.004 0.058 3416 Dihedral : 3.794 14.410 2644 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.77 % Allowed : 14.22 % Favored : 84.02 % 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: 1.56 (0.17), residues: 2408 helix: 1.80 (0.13), residues: 1508 sheet: -1.34 (0.44), residues: 136 loop : 0.05 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 302 TYR 0.018 0.001 TYR A 621 PHE 0.016 0.001 PHE B 553 TRP 0.016 0.001 TRP C 593 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00281 (19860) covalent geometry : angle 0.50916 (26964) hydrogen bonds : bond 0.04147 ( 1129) hydrogen bonds : angle 3.60360 ( 3219) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 304 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 GLU cc_start: 0.7889 (tt0) cc_final: 0.7034 (mm-30) REVERT: A 326 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7736 (ttm110) REVERT: A 381 GLN cc_start: 0.5506 (tp40) cc_final: 0.5117 (mm-40) REVERT: A 491 MET cc_start: 0.8581 (tpp) cc_final: 0.8359 (tpt) REVERT: A 591 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 139 ARG cc_start: 0.7574 (mtp180) cc_final: 0.7228 (mmt-90) REVERT: B 233 GLU cc_start: 0.7848 (tt0) cc_final: 0.6992 (mm-30) REVERT: B 289 GLU cc_start: 0.7060 (pm20) cc_final: 0.6668 (mm-30) REVERT: B 381 GLN cc_start: 0.5552 (tp40) cc_final: 0.5125 (mm-40) REVERT: B 491 MET cc_start: 0.8495 (tpp) cc_final: 0.8241 (tpt) REVERT: C 139 ARG cc_start: 0.7519 (mtp180) cc_final: 0.7174 (mmt-90) REVERT: C 233 GLU cc_start: 0.7865 (tt0) cc_final: 0.7014 (mm-30) REVERT: C 289 GLU cc_start: 0.7160 (pm20) cc_final: 0.6436 (tm-30) REVERT: C 381 GLN cc_start: 0.5580 (tp40) cc_final: 0.5151 (mm-40) REVERT: D 233 GLU cc_start: 0.7877 (tt0) cc_final: 0.7014 (mm-30) REVERT: D 326 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.7754 (ttm110) REVERT: D 381 GLN cc_start: 0.5511 (tp40) cc_final: 0.5122 (mm-40) REVERT: D 491 MET cc_start: 0.8506 (tpp) cc_final: 0.8299 (tpt) outliers start: 37 outliers final: 26 residues processed: 327 average time/residue: 0.6604 time to fit residues: 242.7479 Evaluate side-chains 328 residues out of total 2096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 HIS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 474 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 43 ARG Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain C residue 129 ASN Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 474 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain D residue 157 HIS Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 326 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 591 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 16 optimal weight: 0.0030 chunk 129 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN B 131 ASN B 587 GLN C 131 ASN D 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.178011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.146141 restraints weight = 19604.292| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.90 r_work: 0.3434 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19860 Z= 0.121 Angle : 0.496 8.865 26964 Z= 0.259 Chirality : 0.039 0.126 3072 Planarity : 0.004 0.059 3416 Dihedral : 3.768 14.352 2644 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.67 % Allowed : 14.31 % Favored : 84.02 % 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: 1.54 (0.17), residues: 2408 helix: 1.80 (0.13), residues: 1512 sheet: -1.35 (0.44), residues: 136 loop : -0.00 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 302 TYR 0.013 0.001 TYR D 555 PHE 0.010 0.001 PHE C 534 TRP 0.015 0.001 TRP C 593 HIS 0.003 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00274 (19860) covalent geometry : angle 0.49638 (26964) hydrogen bonds : bond 0.04102 ( 1129) hydrogen bonds : angle 3.59036 ( 3219) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8374.63 seconds wall clock time: 143 minutes 12.81 seconds (8592.81 seconds total)