Starting phenix.real_space_refine on Thu Jun 26 15:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvi_17967/06_2025/8pvi_17967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvi_17967/06_2025/8pvi_17967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pvi_17967/06_2025/8pvi_17967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvi_17967/06_2025/8pvi_17967.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvi_17967/06_2025/8pvi_17967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvi_17967/06_2025/8pvi_17967.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 150 5.16 5 C 19374 2.51 5 N 5442 2.21 5 O 5730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30696 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5116 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Conformer: "B" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} bond proxies already assigned to first conformer: 5202 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 15.90, per 1000 atoms: 0.52 Number of scatterers: 30696 At special positions: 0 Unit cell: (166.327, 177.912, 105.092, 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 150 16.00 O 5730 8.00 N 5442 7.00 C 19374 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: 7.15 Conformation dependent library (CDL) restraints added in 7.8 seconds 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 54 sheets defined 42.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.51 Creating SS restraints... Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS A 51 " --> pdb=" O PHE A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 78 through 88 removed outlier: 4.029A pdb=" N PHE A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 118 Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.095A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 201 " --> pdb=" O ILE A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 356 Processing helix chain 'A' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL A 391 " --> pdb=" O THR A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 525 through 529 Processing helix chain 'A' and resid 548 through 560 Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS B 51 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 Processing helix chain 'B' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 118 Processing helix chain 'B' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 186 through 201 removed outlier: 3.879A pdb=" N THR B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.726A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 293 Processing helix chain 'B' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 356 Processing helix chain 'B' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL B 391 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.954A pdb=" N LYS B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 525 through 529 Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 568 through 574 removed outlier: 3.695A pdb=" N GLU B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.625A pdb=" N MET C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 118 Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY C 201 " --> pdb=" O ILE C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 293 Processing helix chain 'C' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 356 Processing helix chain 'C' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL C 391 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 525 through 529 Processing helix chain 'C' and resid 548 through 560 Processing helix chain 'C' and resid 563 through 568 Processing helix chain 'C' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 596 Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS D 51 " --> pdb=" O PHE D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 78 Processing helix chain 'D' and resid 78 through 88 removed outlier: 4.029A pdb=" N PHE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 118 Processing helix chain 'D' and resid 161 through 174 removed outlier: 4.095A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 192 " --> pdb=" O GLN D 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 201 " --> pdb=" O ILE D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 293 Processing helix chain 'D' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 356 Processing helix chain 'D' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL D 391 " --> pdb=" O THR D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU D 413 " --> pdb=" O GLN D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 525 through 529 Processing helix chain 'D' and resid 548 through 560 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU D 574 " --> pdb=" O ILE D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 583 through 596 Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS E 51 " --> pdb=" O PHE E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.625A pdb=" N MET E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 Processing helix chain 'E' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE E 82 " --> pdb=" O GLU E 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 118 Processing helix chain 'E' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 186 through 201 removed outlier: 3.878A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 192 " --> pdb=" O GLN E 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY E 201 " --> pdb=" O ILE E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.725A pdb=" N LEU E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 293 Processing helix chain 'E' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 356 Processing helix chain 'E' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL E 391 " --> pdb=" O THR E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU E 413 " --> pdb=" O GLN E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 Processing helix chain 'E' and resid 453 through 458 removed outlier: 3.955A pdb=" N LYS E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL E 490 " --> pdb=" O GLY E 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS E 492 " --> pdb=" O ARG E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 511 Processing helix chain 'E' and resid 525 through 529 Processing helix chain 'E' and resid 548 through 560 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 568 through 574 removed outlier: 3.696A pdb=" N GLU E 574 " --> pdb=" O ILE E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 Processing helix chain 'F' and resid 40 through 51 removed outlier: 3.526A pdb=" N LYS F 51 " --> pdb=" O PHE F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.626A pdb=" N MET F 59 " --> pdb=" O ALA F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 78 Processing helix chain 'F' and resid 78 through 88 removed outlier: 4.030A pdb=" N PHE F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN F 88 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 118 Processing helix chain 'F' and resid 161 through 174 removed outlier: 4.094A pdb=" N LYS F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Proline residue: F 170 - end of helix Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 186 through 201 removed outlier: 3.879A pdb=" N THR F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY F 201 " --> pdb=" O ILE F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.726A pdb=" N LEU F 222 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 242 removed outlier: 3.505A pdb=" N VAL F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 273 through 289 removed outlier: 4.010A pdb=" N ALA F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 293 Processing helix chain 'F' and resid 307 through 321 removed outlier: 3.532A pdb=" N VAL F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 356 Processing helix chain 'F' and resid 388 through 393 removed outlier: 3.678A pdb=" N VAL F 391 " --> pdb=" O THR F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 418 removed outlier: 3.920A pdb=" N LEU F 413 " --> pdb=" O GLN F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 Processing helix chain 'F' and resid 453 through 458 removed outlier: 3.954A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 486 through 492 removed outlier: 4.134A pdb=" N VAL F 490 " --> pdb=" O GLY F 486 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 511 Processing helix chain 'F' and resid 525 through 529 Processing helix chain 'F' and resid 548 through 560 Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 568 through 574 removed outlier: 3.695A pdb=" N GLU F 574 " --> pdb=" O ILE F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 596 Processing sheet with id=1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=2, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=3, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=4, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=5, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 228 " --> pdb=" O THR A 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU A 256 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE A 230 " --> pdb=" O GLU A 256 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU A 379 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN A 261 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE A 301 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS A 263 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL A 303 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 265 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 262 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 423 " --> pdb=" O HIS A 446 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 472 through 473 Processing sheet with id=8, first strand: chain 'A' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU A 520 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU A 541 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP A 538 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL A 626 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 656 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 628 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 654 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 630 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA A 652 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 647 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 671 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 649 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 669 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP A 651 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 667 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 653 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 665 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 655 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER A 667 " --> pdb=" O GLY A 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY A 608 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 669 " --> pdb=" O ASN A 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN A 606 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 671 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'A' and resid 545 through 546 removed outlier: 5.564A pdb=" N VAL A 626 " --> pdb=" O PHE A 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE A 656 " --> pdb=" O VAL A 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU A 628 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU A 654 " --> pdb=" O LEU A 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS A 630 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA A 652 " --> pdb=" O CYS A 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 647 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 671 " --> pdb=" O GLY A 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 649 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 669 " --> pdb=" O VAL A 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP A 651 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 667 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 653 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU A 665 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 655 " --> pdb=" O VAL A 663 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 665 " --> pdb=" O ARG A 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 613 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=11, first strand: chain 'B' and resid 20 through 23 Processing sheet with id=12, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=13, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=14, first strand: chain 'B' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 228 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU B 256 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B 230 " --> pdb=" O GLU B 256 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU B 379 " --> pdb=" O ARG B 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG B 299 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN B 261 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE B 301 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS B 263 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B 303 " --> pdb=" O CYS B 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 265 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS B 262 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU B 423 " --> pdb=" O HIS B 446 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'B' and resid 472 through 473 Processing sheet with id=17, first strand: chain 'B' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU B 520 " --> pdb=" O SER B 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 541 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP B 538 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY B 647 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 671 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 649 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU B 669 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP B 651 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 667 " --> pdb=" O TRP B 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 653 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 665 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 655 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER B 667 " --> pdb=" O GLY B 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY B 608 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 669 " --> pdb=" O ASN B 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN B 606 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 671 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'B' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY B 647 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU B 671 " --> pdb=" O GLY B 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 649 " --> pdb=" O LEU B 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU B 669 " --> pdb=" O VAL B 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP B 651 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER B 667 " --> pdb=" O TRP B 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL B 653 " --> pdb=" O LEU B 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 665 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 655 " --> pdb=" O VAL B 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU B 665 " --> pdb=" O ARG B 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 613 " --> pdb=" O LEU B 665 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=20, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=21, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=22, first strand: chain 'C' and resid 124 through 125 Processing sheet with id=23, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA C 151 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS C 181 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS C 153 " --> pdb=" O LYS C 181 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 228 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU C 256 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE C 230 " --> pdb=" O GLU C 256 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU C 379 " --> pdb=" O ARG C 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG C 299 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN C 261 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE C 301 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS C 263 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL C 303 " --> pdb=" O CYS C 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 265 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS C 262 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU C 423 " --> pdb=" O HIS C 446 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'C' and resid 472 through 473 Processing sheet with id=26, first strand: chain 'C' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU C 520 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 541 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP C 538 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL C 626 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE C 656 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 628 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU C 654 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS C 630 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA C 652 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY C 647 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 671 " --> pdb=" O GLY C 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 649 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 669 " --> pdb=" O VAL C 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP C 651 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 667 " --> pdb=" O TRP C 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 653 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 665 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 655 " --> pdb=" O VAL C 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER C 667 " --> pdb=" O GLY C 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY C 608 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU C 669 " --> pdb=" O ASN C 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN C 606 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 671 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'C' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL C 626 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE C 656 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 628 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU C 654 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS C 630 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA C 652 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY C 647 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 671 " --> pdb=" O GLY C 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 649 " --> pdb=" O LEU C 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU C 669 " --> pdb=" O VAL C 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP C 651 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER C 667 " --> pdb=" O TRP C 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 653 " --> pdb=" O LEU C 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 665 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 655 " --> pdb=" O VAL C 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 665 " --> pdb=" O ARG C 613 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG C 613 " --> pdb=" O LEU C 665 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=29, first strand: chain 'D' and resid 20 through 23 Processing sheet with id=30, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=31, first strand: chain 'D' and resid 124 through 125 Processing sheet with id=32, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA D 151 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS D 181 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS D 153 " --> pdb=" O LYS D 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL D 228 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU D 256 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE D 230 " --> pdb=" O GLU D 256 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU D 379 " --> pdb=" O ARG D 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG D 299 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN D 261 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE D 301 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS D 263 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL D 303 " --> pdb=" O CYS D 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU D 265 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS D 262 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU D 423 " --> pdb=" O HIS D 446 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'D' and resid 472 through 473 Processing sheet with id=35, first strand: chain 'D' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU D 520 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU D 541 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP D 538 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL D 626 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE D 656 " --> pdb=" O VAL D 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 628 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU D 654 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS D 630 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA D 652 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY D 647 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 671 " --> pdb=" O GLY D 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 649 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 669 " --> pdb=" O VAL D 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP D 651 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 667 " --> pdb=" O TRP D 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 653 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 665 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 655 " --> pdb=" O VAL D 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER D 667 " --> pdb=" O GLY D 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY D 608 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU D 669 " --> pdb=" O ASN D 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN D 606 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU D 671 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'D' and resid 545 through 546 removed outlier: 5.564A pdb=" N VAL D 626 " --> pdb=" O PHE D 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE D 656 " --> pdb=" O VAL D 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 628 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLU D 654 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS D 630 " --> pdb=" O ALA D 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA D 652 " --> pdb=" O CYS D 630 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY D 647 " --> pdb=" O LEU D 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 671 " --> pdb=" O GLY D 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 649 " --> pdb=" O LEU D 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 669 " --> pdb=" O VAL D 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP D 651 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER D 667 " --> pdb=" O TRP D 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL D 653 " --> pdb=" O LEU D 665 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 665 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D 655 " --> pdb=" O VAL D 663 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 665 " --> pdb=" O ARG D 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG D 613 " --> pdb=" O LEU D 665 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=38, first strand: chain 'E' and resid 20 through 23 Processing sheet with id=39, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=40, first strand: chain 'E' and resid 124 through 125 Processing sheet with id=41, first strand: chain 'E' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA E 151 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS E 181 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N HIS E 153 " --> pdb=" O LYS E 181 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL E 228 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU E 256 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE E 230 " --> pdb=" O GLU E 256 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'E' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU E 379 " --> pdb=" O ARG E 361 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ARG E 299 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN E 261 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ILE E 301 " --> pdb=" O ASN E 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS E 263 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL E 303 " --> pdb=" O CYS E 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU E 265 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS E 262 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU E 423 " --> pdb=" O HIS E 446 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'E' and resid 472 through 473 Processing sheet with id=44, first strand: chain 'E' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU E 520 " --> pdb=" O SER E 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU E 541 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ASP E 538 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY E 647 " --> pdb=" O LEU E 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU E 671 " --> pdb=" O GLY E 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL E 649 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E 669 " --> pdb=" O VAL E 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP E 651 " --> pdb=" O SER E 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER E 667 " --> pdb=" O TRP E 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 653 " --> pdb=" O LEU E 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 665 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 655 " --> pdb=" O VAL E 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER E 667 " --> pdb=" O GLY E 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY E 608 " --> pdb=" O SER E 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU E 669 " --> pdb=" O ASN E 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN E 606 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU E 671 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'E' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY E 647 " --> pdb=" O LEU E 671 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU E 671 " --> pdb=" O GLY E 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL E 649 " --> pdb=" O LEU E 669 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E 669 " --> pdb=" O VAL E 649 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N TRP E 651 " --> pdb=" O SER E 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER E 667 " --> pdb=" O TRP E 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL E 653 " --> pdb=" O LEU E 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 665 " --> pdb=" O VAL E 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL E 655 " --> pdb=" O VAL E 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU E 665 " --> pdb=" O ARG E 613 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 613 " --> pdb=" O LEU E 665 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=47, first strand: chain 'F' and resid 20 through 23 Processing sheet with id=48, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=49, first strand: chain 'F' and resid 124 through 125 Processing sheet with id=50, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.149A pdb=" N ALA F 151 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS F 181 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N HIS F 153 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL F 228 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N GLU F 256 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE F 230 " --> pdb=" O GLU F 256 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'F' and resid 359 through 362 removed outlier: 6.254A pdb=" N LEU F 379 " --> pdb=" O ARG F 361 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG F 299 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN F 261 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE F 301 " --> pdb=" O ASN F 261 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS F 263 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL F 303 " --> pdb=" O CYS F 263 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU F 265 " --> pdb=" O VAL F 303 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS F 262 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU F 423 " --> pdb=" O HIS F 446 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'F' and resid 472 through 473 Processing sheet with id=53, first strand: chain 'F' and resid 520 through 521 removed outlier: 5.883A pdb=" N GLU F 520 " --> pdb=" O SER F 539 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU F 541 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP F 538 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N VAL F 626 " --> pdb=" O PHE F 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE F 656 " --> pdb=" O VAL F 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU F 628 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU F 654 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS F 630 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA F 652 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY F 647 " --> pdb=" O LEU F 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU F 671 " --> pdb=" O GLY F 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 649 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU F 669 " --> pdb=" O VAL F 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP F 651 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER F 667 " --> pdb=" O TRP F 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL F 653 " --> pdb=" O LEU F 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU F 665 " --> pdb=" O VAL F 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 655 " --> pdb=" O VAL F 663 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER F 667 " --> pdb=" O GLY F 608 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY F 608 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU F 669 " --> pdb=" O ASN F 606 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASN F 606 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU F 671 " --> pdb=" O ILE F 604 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'F' and resid 545 through 546 removed outlier: 5.563A pdb=" N VAL F 626 " --> pdb=" O PHE F 656 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N PHE F 656 " --> pdb=" O VAL F 626 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU F 628 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N GLU F 654 " --> pdb=" O LEU F 628 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS F 630 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ALA F 652 " --> pdb=" O CYS F 630 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLY F 647 " --> pdb=" O LEU F 671 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LEU F 671 " --> pdb=" O GLY F 647 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL F 649 " --> pdb=" O LEU F 669 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU F 669 " --> pdb=" O VAL F 649 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N TRP F 651 " --> pdb=" O SER F 667 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER F 667 " --> pdb=" O TRP F 651 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL F 653 " --> pdb=" O LEU F 665 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU F 665 " --> pdb=" O VAL F 653 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL F 655 " --> pdb=" O VAL F 663 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 665 " --> pdb=" O ARG F 613 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 613 " --> pdb=" O LEU F 665 " (cutoff:3.500A) 1386 hydrogen bonds defined for protein. 3834 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: 14.02 Time building geometry restraints manager: 8.50 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: 7639 1.34 - 1.47: 9579 1.47 - 1.59: 13862 1.59 - 1.72: 0 1.72 - 1.85: 240 Bond restraints: 31320 Sorted by residual: bond pdb=" C SER F 465 " pdb=" N PRO F 466 " ideal model delta sigma weight residual 1.335 1.373 -0.038 8.70e-03 1.32e+04 1.86e+01 bond pdb=" C SER B 465 " pdb=" N PRO B 466 " ideal model delta sigma weight residual 1.335 1.373 -0.038 8.70e-03 1.32e+04 1.86e+01 bond pdb=" C SER D 465 " pdb=" N PRO D 466 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.85e+01 bond pdb=" C SER A 465 " pdb=" N PRO A 466 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.85e+01 bond pdb=" C SER E 465 " pdb=" N PRO E 466 " ideal model delta sigma weight residual 1.335 1.372 -0.037 8.70e-03 1.32e+04 1.83e+01 ... (remaining 31315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 32017 1.78 - 3.55: 9018 3.55 - 5.33: 1217 5.33 - 7.10: 234 7.10 - 8.88: 30 Bond angle restraints: 42516 Sorted by residual: angle pdb=" CB GLU D 348 " pdb=" CG GLU D 348 " pdb=" CD GLU D 348 " ideal model delta sigma weight residual 112.60 121.48 -8.88 1.70e+00 3.46e-01 2.73e+01 angle pdb=" CB GLU A 348 " pdb=" CG GLU A 348 " pdb=" CD GLU A 348 " ideal model delta sigma weight residual 112.60 121.48 -8.88 1.70e+00 3.46e-01 2.73e+01 angle pdb=" CB GLU F 348 " pdb=" CG GLU F 348 " pdb=" CD GLU F 348 " ideal model delta sigma weight residual 112.60 121.46 -8.86 1.70e+00 3.46e-01 2.72e+01 angle pdb=" CB GLU B 348 " pdb=" CG GLU B 348 " pdb=" CD GLU B 348 " ideal model delta sigma weight residual 112.60 121.46 -8.86 1.70e+00 3.46e-01 2.72e+01 angle pdb=" CB GLU E 348 " pdb=" CG GLU E 348 " pdb=" CD GLU E 348 " ideal model delta sigma weight residual 112.60 121.45 -8.85 1.70e+00 3.46e-01 2.71e+01 ... (remaining 42511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 16796 16.59 - 33.19: 1472 33.19 - 49.78: 362 49.78 - 66.37: 126 66.37 - 82.97: 84 Dihedral angle restraints: 18840 sinusoidal: 7296 harmonic: 11544 Sorted by residual: dihedral pdb=" CA THR A 542 " pdb=" C THR A 542 " pdb=" N PRO A 543 " pdb=" CA PRO A 543 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR D 542 " pdb=" C THR D 542 " pdb=" N PRO D 543 " pdb=" CA PRO D 543 " ideal model delta harmonic sigma weight residual 180.00 159.77 20.23 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA THR E 542 " pdb=" C THR E 542 " pdb=" N PRO E 543 " pdb=" CA PRO E 543 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 18837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2322 0.047 - 0.093: 1375 0.093 - 0.140: 749 0.140 - 0.187: 312 0.187 - 0.233: 84 Chirality restraints: 4842 Sorted by residual: chirality pdb=" CB ILE C 280 " pdb=" CA ILE C 280 " pdb=" CG1 ILE C 280 " pdb=" CG2 ILE C 280 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE E 280 " pdb=" CA ILE E 280 " pdb=" CG1 ILE E 280 " pdb=" CG2 ILE E 280 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB ILE B 280 " pdb=" CA ILE B 280 " pdb=" CG1 ILE B 280 " pdb=" CG2 ILE B 280 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4839 not shown) Planarity restraints: 5580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 470 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C LEU E 470 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU E 470 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL E 471 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 470 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.75e+00 pdb=" C LEU C 470 " 0.041 2.00e-02 2.50e+03 pdb=" O LEU C 470 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL C 471 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 470 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.65e+00 pdb=" C LEU A 470 " -0.041 2.00e-02 2.50e+03 pdb=" O LEU A 470 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 471 " 0.014 2.00e-02 2.50e+03 ... (remaining 5577 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 8669 2.85 - 3.36: 28417 3.36 - 3.87: 53344 3.87 - 4.39: 62060 4.39 - 4.90: 105165 Nonbonded interactions: 257655 Sorted by model distance: nonbonded pdb=" O ASN F 158 " pdb=" NZ LYS F 290 " model vdw 2.334 3.120 nonbonded pdb=" O ASN B 158 " pdb=" NZ LYS B 290 " model vdw 2.334 3.120 nonbonded pdb=" O ASN D 158 " pdb=" NZ LYS D 290 " model vdw 2.335 3.120 nonbonded pdb=" O ASN A 158 " pdb=" NZ LYS A 290 " model vdw 2.335 3.120 nonbonded pdb=" O ASN E 158 " pdb=" NZ LYS E 290 " model vdw 2.335 3.120 ... (remaining 257650 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: 0.26 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.350 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: 0.050 Extract box with map and model: 1.260 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 74.610 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.010 0.043 31320 Z= 0.643 Angle : 1.623 8.876 42516 Z= 1.084 Chirality : 0.078 0.233 4842 Planarity : 0.007 0.047 5580 Dihedral : 15.333 82.966 11424 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.48 % Favored : 98.37 % Rotamer: Outliers : 1.13 % Allowed : 8.87 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.12), residues: 4062 helix: 0.26 (0.13), residues: 1416 sheet: 0.97 (0.20), residues: 756 loop : -0.36 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.005 TRP B 172 HIS 0.012 0.003 HIS A 562 PHE 0.032 0.007 PHE B 586 TYR 0.027 0.008 TYR E 110 ARG 0.021 0.004 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.15640 ( 1344) hydrogen bonds : angle 6.69551 ( 3834) covalent geometry : bond 0.00989 (31320) covalent geometry : angle 1.62297 (42516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 782 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 HIS cc_start: 0.6455 (t-90) cc_final: 0.5788 (t-170) REVERT: A 93 ARG cc_start: 0.7103 (mmm160) cc_final: 0.6667 (tpt-90) REVERT: A 158 ASN cc_start: 0.7981 (OUTLIER) cc_final: 0.7731 (m-40) REVERT: A 196 SER cc_start: 0.8620 (m) cc_final: 0.8224 (t) REVERT: A 251 ILE cc_start: 0.9006 (mt) cc_final: 0.8790 (mm) REVERT: A 255 MET cc_start: 0.6195 (ttp) cc_final: 0.5988 (ptt) REVERT: A 273 GLN cc_start: 0.7635 (mt0) cc_final: 0.7374 (mt0) REVERT: A 410 ARG cc_start: 0.7651 (ttm-80) cc_final: 0.7160 (mpt180) REVERT: A 411 HIS cc_start: 0.7193 (t-90) cc_final: 0.6834 (t-90) REVERT: A 434 ILE cc_start: 0.6956 (mm) cc_final: 0.6610 (mt) REVERT: A 441 ASP cc_start: 0.8327 (m-30) cc_final: 0.7557 (m-30) REVERT: A 528 ARG cc_start: 0.7422 (mtt-85) cc_final: 0.7052 (mmm160) REVERT: A 610 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7145 (tp30) REVERT: A 622 ASP cc_start: 0.7244 (m-30) cc_final: 0.6964 (m-30) REVERT: B 74 HIS cc_start: 0.6530 (t-90) cc_final: 0.5357 (t70) REVERT: B 93 ARG cc_start: 0.7058 (mmm160) cc_final: 0.6329 (tpp80) REVERT: B 158 ASN cc_start: 0.7904 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: B 251 ILE cc_start: 0.8999 (mt) cc_final: 0.8792 (mm) REVERT: B 273 GLN cc_start: 0.7826 (mt0) cc_final: 0.7545 (mt0) REVERT: B 293 GLN cc_start: 0.6160 (mt0) cc_final: 0.5513 (mm-40) REVERT: B 410 ARG cc_start: 0.7740 (ttm-80) cc_final: 0.7269 (mpt180) REVERT: B 411 HIS cc_start: 0.7315 (t-90) cc_final: 0.6951 (t-90) REVERT: B 434 ILE cc_start: 0.6930 (mm) cc_final: 0.6565 (mt) REVERT: B 441 ASP cc_start: 0.8363 (m-30) cc_final: 0.7605 (m-30) REVERT: B 528 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6979 (mmm160) REVERT: B 568 ASP cc_start: 0.7790 (t0) cc_final: 0.7568 (t0) REVERT: B 607 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.7990 (p90) REVERT: B 610 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7219 (tp30) REVERT: C 29 GLU cc_start: 0.7237 (pt0) cc_final: 0.6999 (tt0) REVERT: C 60 THR cc_start: 0.8036 (p) cc_final: 0.7746 (t) REVERT: C 74 HIS cc_start: 0.6437 (t-90) cc_final: 0.5222 (t70) REVERT: C 158 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7649 (m-40) REVERT: C 176 MET cc_start: 0.8899 (mtp) cc_final: 0.8690 (ttm) REVERT: C 236 THR cc_start: 0.6571 (m) cc_final: 0.6364 (p) REVERT: C 255 MET cc_start: 0.6292 (ttp) cc_final: 0.5937 (ttp) REVERT: C 273 GLN cc_start: 0.7768 (mt0) cc_final: 0.7514 (mt0) REVERT: C 293 GLN cc_start: 0.6226 (mt0) cc_final: 0.5499 (mm-40) REVERT: C 410 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7246 (mpt180) REVERT: C 411 HIS cc_start: 0.7418 (t-90) cc_final: 0.6907 (t-90) REVERT: C 434 ILE cc_start: 0.6730 (mm) cc_final: 0.6315 (mt) REVERT: C 441 ASP cc_start: 0.8302 (m-30) cc_final: 0.7472 (m-30) REVERT: C 528 ARG cc_start: 0.7300 (mtt-85) cc_final: 0.7009 (mmm160) REVERT: C 567 MET cc_start: 0.8102 (mmm) cc_final: 0.7818 (mmt) REVERT: C 568 ASP cc_start: 0.7734 (t0) cc_final: 0.7510 (t0) REVERT: C 607 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.8330 (p90) REVERT: C 610 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7391 (tp30) REVERT: C 622 ASP cc_start: 0.7299 (m-30) cc_final: 0.6956 (m-30) REVERT: D 74 HIS cc_start: 0.6452 (t-90) cc_final: 0.5785 (t-170) REVERT: D 93 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6666 (tpt-90) REVERT: D 158 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7734 (m-40) REVERT: D 196 SER cc_start: 0.8620 (m) cc_final: 0.8220 (t) REVERT: D 251 ILE cc_start: 0.9007 (mt) cc_final: 0.8793 (mm) REVERT: D 255 MET cc_start: 0.6204 (ttp) cc_final: 0.5987 (ptt) REVERT: D 273 GLN cc_start: 0.7633 (mt0) cc_final: 0.7372 (mt0) REVERT: D 410 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7161 (mpt180) REVERT: D 411 HIS cc_start: 0.7195 (t-90) cc_final: 0.6838 (t-90) REVERT: D 434 ILE cc_start: 0.6955 (mm) cc_final: 0.6615 (mt) REVERT: D 441 ASP cc_start: 0.8326 (m-30) cc_final: 0.7547 (m-30) REVERT: D 528 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7051 (mmm160) REVERT: D 610 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7145 (tp30) REVERT: D 622 ASP cc_start: 0.7243 (m-30) cc_final: 0.6964 (m-30) REVERT: E 29 GLU cc_start: 0.7208 (pt0) cc_final: 0.6967 (tt0) REVERT: E 60 THR cc_start: 0.8038 (p) cc_final: 0.7746 (t) REVERT: E 74 HIS cc_start: 0.6431 (t-90) cc_final: 0.5219 (t70) REVERT: E 158 ASN cc_start: 0.7948 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: E 176 MET cc_start: 0.8898 (mtp) cc_final: 0.8690 (ttm) REVERT: E 236 THR cc_start: 0.6572 (m) cc_final: 0.6362 (p) REVERT: E 255 MET cc_start: 0.6283 (ttp) cc_final: 0.5932 (ttp) REVERT: E 273 GLN cc_start: 0.7768 (mt0) cc_final: 0.7516 (mt0) REVERT: E 293 GLN cc_start: 0.6228 (mt0) cc_final: 0.5501 (mm-40) REVERT: E 410 ARG cc_start: 0.7695 (ttm-80) cc_final: 0.7248 (mpt180) REVERT: E 411 HIS cc_start: 0.7416 (t-90) cc_final: 0.6909 (t-90) REVERT: E 434 ILE cc_start: 0.6729 (mm) cc_final: 0.6312 (mt) REVERT: E 441 ASP cc_start: 0.8303 (m-30) cc_final: 0.7471 (m-30) REVERT: E 528 ARG cc_start: 0.7297 (mtt-85) cc_final: 0.7005 (mmm160) REVERT: E 567 MET cc_start: 0.8099 (mmm) cc_final: 0.7813 (mmt) REVERT: E 568 ASP cc_start: 0.7734 (t0) cc_final: 0.7509 (t0) REVERT: E 607 TYR cc_start: 0.8730 (OUTLIER) cc_final: 0.8328 (p90) REVERT: E 610 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7393 (tp30) REVERT: E 622 ASP cc_start: 0.7300 (m-30) cc_final: 0.6957 (m-30) REVERT: F 74 HIS cc_start: 0.6531 (t-90) cc_final: 0.5355 (t70) REVERT: F 93 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6326 (tpp80) REVERT: F 158 ASN cc_start: 0.7906 (OUTLIER) cc_final: 0.7445 (m-40) REVERT: F 251 ILE cc_start: 0.9000 (mt) cc_final: 0.8794 (mm) REVERT: F 273 GLN cc_start: 0.7831 (mt0) cc_final: 0.7548 (mt0) REVERT: F 293 GLN cc_start: 0.6152 (mt0) cc_final: 0.5512 (mm-40) REVERT: F 410 ARG cc_start: 0.7699 (ttm-80) cc_final: 0.7225 (mpt180) REVERT: F 411 HIS cc_start: 0.7310 (t-90) cc_final: 0.6946 (t-90) REVERT: F 434 ILE cc_start: 0.6925 (mm) cc_final: 0.6563 (mt) REVERT: F 441 ASP cc_start: 0.8363 (m-30) cc_final: 0.7603 (m-30) REVERT: F 528 ARG cc_start: 0.7271 (mtt-85) cc_final: 0.6981 (mmm160) REVERT: F 568 ASP cc_start: 0.7784 (t0) cc_final: 0.7563 (t0) REVERT: F 607 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7988 (p90) REVERT: F 610 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7217 (tp30) outliers start: 36 outliers final: 6 residues processed: 794 average time/residue: 0.4883 time to fit residues: 593.4959 Evaluate side-chains 408 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 392 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 158 ASN Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 158 ASN Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 607 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 339 optimal weight: 4.9990 chunk 304 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 162 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 365 optimal weight: 0.4980 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN A 566 HIS A 676 HIS B 409 GLN B 450 GLN B 566 HIS B 659 HIS B 676 HIS C 409 GLN C 566 HIS C 659 HIS ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN D 566 HIS E 409 GLN E 566 HIS E 659 HIS F 409 GLN F 450 GLN F 566 HIS F 659 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.092738 restraints weight = 101524.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.094200 restraints weight = 65436.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095054 restraints weight = 54396.525| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31320 Z= 0.218 Angle : 0.707 13.541 42516 Z= 0.365 Chirality : 0.046 0.172 4842 Planarity : 0.005 0.042 5580 Dihedral : 5.172 41.142 4382 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.27 % Allowed : 12.11 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4062 helix: 1.02 (0.13), residues: 1452 sheet: 1.00 (0.19), residues: 786 loop : -0.40 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 651 HIS 0.006 0.002 HIS C 463 PHE 0.026 0.002 PHE E 595 TYR 0.025 0.002 TYR C 607 ARG 0.007 0.001 ARG E 241 Details of bonding type rmsd hydrogen bonds : bond 0.04481 ( 1344) hydrogen bonds : angle 5.19399 ( 3834) covalent geometry : bond 0.00505 (31320) covalent geometry : angle 0.70682 (42516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 380 time to evaluate : 3.543 Fit side-chains REVERT: A 93 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7533 (tpt-90) REVERT: A 256 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6350 (mp0) REVERT: A 610 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6905 (tp30) REVERT: A 622 ASP cc_start: 0.7663 (m-30) cc_final: 0.7247 (m-30) REVERT: B 93 ARG cc_start: 0.7977 (mmm160) cc_final: 0.7547 (tpt-90) REVERT: B 158 ASN cc_start: 0.8346 (m-40) cc_final: 0.8115 (m-40) REVERT: B 256 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: B 293 GLN cc_start: 0.7179 (mt0) cc_final: 0.6817 (mt0) REVERT: B 411 HIS cc_start: 0.7588 (t-90) cc_final: 0.7083 (t-90) REVERT: B 607 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8925 (p90) REVERT: B 610 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6982 (tp30) REVERT: C 93 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7458 (tpt170) REVERT: C 158 ASN cc_start: 0.8427 (m-40) cc_final: 0.8122 (m-40) REVERT: C 164 MET cc_start: 0.7192 (ttp) cc_final: 0.6905 (ttt) REVERT: C 293 GLN cc_start: 0.7247 (mt0) cc_final: 0.6931 (mt0) REVERT: C 411 HIS cc_start: 0.7618 (t-90) cc_final: 0.7112 (t-90) REVERT: C 567 MET cc_start: 0.7713 (mmm) cc_final: 0.7509 (mmt) REVERT: C 607 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.9106 (p90) REVERT: C 610 GLU cc_start: 0.7375 (mm-30) cc_final: 0.6957 (tp30) REVERT: C 622 ASP cc_start: 0.7724 (m-30) cc_final: 0.7523 (m-30) REVERT: D 93 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7531 (tpt-90) REVERT: D 256 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: D 610 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6911 (tp30) REVERT: D 622 ASP cc_start: 0.7663 (m-30) cc_final: 0.7245 (m-30) REVERT: E 93 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7461 (tpt170) REVERT: E 158 ASN cc_start: 0.8433 (m-40) cc_final: 0.8129 (m-40) REVERT: E 164 MET cc_start: 0.7184 (ttp) cc_final: 0.6896 (ttt) REVERT: E 293 GLN cc_start: 0.7234 (mt0) cc_final: 0.6929 (mt0) REVERT: E 411 HIS cc_start: 0.7611 (t-90) cc_final: 0.7111 (t-90) REVERT: E 567 MET cc_start: 0.7709 (mmm) cc_final: 0.7504 (mmt) REVERT: E 607 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.9107 (p90) REVERT: E 610 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6954 (tp30) REVERT: E 622 ASP cc_start: 0.7714 (m-30) cc_final: 0.7510 (m-30) REVERT: F 93 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7552 (tpt-90) REVERT: F 158 ASN cc_start: 0.8340 (m-40) cc_final: 0.8115 (m-40) REVERT: F 256 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: F 293 GLN cc_start: 0.7176 (mt0) cc_final: 0.6813 (mt0) REVERT: F 411 HIS cc_start: 0.7605 (t-90) cc_final: 0.7087 (t-90) REVERT: F 607 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.8929 (p90) REVERT: F 610 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6984 (tp30) outliers start: 104 outliers final: 42 residues processed: 458 average time/residue: 0.4399 time to fit residues: 323.3223 Evaluate side-chains 330 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 280 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 256 GLU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 663 VAL Chi-restraints excluded: chain F residue 670 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 375 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 268 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 GLN A 659 HIS B 74 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN D 659 HIS E 273 GLN ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN F 74 HIS ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.116694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094721 restraints weight = 92816.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094670 restraints weight = 66849.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096088 restraints weight = 56306.030| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31320 Z= 0.136 Angle : 0.598 11.806 42516 Z= 0.310 Chirality : 0.043 0.209 4842 Planarity : 0.004 0.034 5580 Dihedral : 4.720 40.340 4358 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.52 % Allowed : 13.36 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.13), residues: 4062 helix: 1.29 (0.13), residues: 1446 sheet: 0.88 (0.19), residues: 786 loop : -0.35 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 172 HIS 0.004 0.001 HIS C 463 PHE 0.026 0.002 PHE F 595 TYR 0.021 0.002 TYR B 607 ARG 0.007 0.001 ARG F 410 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 1344) hydrogen bonds : angle 4.89110 ( 3834) covalent geometry : bond 0.00310 (31320) covalent geometry : angle 0.59765 (42516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 323 time to evaluate : 3.220 Fit side-chains REVERT: A 93 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7561 (tpt-90) REVERT: A 95 ASP cc_start: 0.7517 (m-30) cc_final: 0.7229 (m-30) REVERT: A 256 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: A 567 MET cc_start: 0.7685 (mmm) cc_final: 0.7176 (mmt) REVERT: A 610 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6796 (tp30) REVERT: A 622 ASP cc_start: 0.7491 (m-30) cc_final: 0.7201 (m-30) REVERT: B 93 ARG cc_start: 0.7973 (mmm160) cc_final: 0.7627 (tpt-90) REVERT: B 607 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8844 (p90) REVERT: B 610 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6878 (tp30) REVERT: C 8 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7503 (pp) REVERT: C 93 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7748 (tpt-90) REVERT: C 158 ASN cc_start: 0.8490 (m-40) cc_final: 0.8154 (m-40) REVERT: C 176 MET cc_start: 0.8343 (mtp) cc_final: 0.8116 (ttt) REVERT: C 256 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6271 (mp0) REVERT: C 293 GLN cc_start: 0.6966 (mt0) cc_final: 0.6747 (mm-40) REVERT: C 411 HIS cc_start: 0.7541 (t-90) cc_final: 0.6986 (t-90) REVERT: C 607 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.9001 (p90) REVERT: C 610 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6874 (tp30) REVERT: C 622 ASP cc_start: 0.7607 (m-30) cc_final: 0.7375 (m-30) REVERT: D 93 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7567 (tpt-90) REVERT: D 95 ASP cc_start: 0.7512 (m-30) cc_final: 0.7228 (m-30) REVERT: D 256 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: D 567 MET cc_start: 0.7697 (mmm) cc_final: 0.7181 (mmt) REVERT: D 610 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6804 (tp30) REVERT: D 622 ASP cc_start: 0.7488 (m-30) cc_final: 0.7191 (m-30) REVERT: E 8 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7514 (pp) REVERT: E 93 ARG cc_start: 0.8034 (mmm160) cc_final: 0.7752 (tpt-90) REVERT: E 158 ASN cc_start: 0.8476 (m-40) cc_final: 0.8155 (m-40) REVERT: E 176 MET cc_start: 0.8349 (mtp) cc_final: 0.8127 (ttt) REVERT: E 256 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: E 293 GLN cc_start: 0.6943 (mt0) cc_final: 0.6742 (mm-40) REVERT: E 411 HIS cc_start: 0.7538 (t-90) cc_final: 0.6989 (t-90) REVERT: E 607 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.9007 (p90) REVERT: E 610 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6851 (tp30) REVERT: E 622 ASP cc_start: 0.7589 (m-30) cc_final: 0.7358 (m-30) REVERT: F 93 ARG cc_start: 0.7975 (mmm160) cc_final: 0.7634 (tpt-90) REVERT: F 607 TYR cc_start: 0.9294 (OUTLIER) cc_final: 0.8845 (p90) REVERT: F 610 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6888 (tp30) outliers start: 80 outliers final: 40 residues processed: 377 average time/residue: 0.4171 time to fit residues: 254.0096 Evaluate side-chains 316 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 266 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 182 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 224 optimal weight: 0.2980 chunk 389 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 314 optimal weight: 0.8980 chunk 365 optimal weight: 7.9990 chunk 326 optimal weight: 1.9990 chunk 156 optimal weight: 8.9990 chunk 397 optimal weight: 4.9990 chunk 302 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN C 74 HIS ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 HIS E 74 HIS ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 414 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093862 restraints weight = 92447.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.094206 restraints weight = 64708.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095469 restraints weight = 54003.668| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31320 Z= 0.146 Angle : 0.587 10.050 42516 Z= 0.303 Chirality : 0.043 0.196 4842 Planarity : 0.004 0.035 5580 Dihedral : 4.651 41.058 4358 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.77 % Allowed : 14.28 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.13), residues: 4062 helix: 1.15 (0.13), residues: 1488 sheet: 0.90 (0.18), residues: 780 loop : -0.36 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 172 HIS 0.004 0.001 HIS F 463 PHE 0.024 0.002 PHE D 595 TYR 0.022 0.002 TYR B 607 ARG 0.003 0.000 ARG C 281 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 1344) hydrogen bonds : angle 4.78903 ( 3834) covalent geometry : bond 0.00341 (31320) covalent geometry : angle 0.58679 (42516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 282 time to evaluate : 3.649 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7561 (tpt-90) REVERT: A 95 ASP cc_start: 0.7515 (m-30) cc_final: 0.7228 (m-30) REVERT: A 256 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6325 (mp0) REVERT: A 567 MET cc_start: 0.7702 (mmm) cc_final: 0.7482 (mmt) REVERT: A 610 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6731 (tp30) REVERT: A 622 ASP cc_start: 0.7645 (m-30) cc_final: 0.7229 (m-30) REVERT: B 93 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7646 (tpt-90) REVERT: B 567 MET cc_start: 0.7793 (mmm) cc_final: 0.7547 (mmt) REVERT: B 607 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8909 (p90) REVERT: B 610 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6860 (tp30) REVERT: C 8 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7678 (pp) REVERT: C 93 ARG cc_start: 0.8063 (mmm160) cc_final: 0.7580 (tpt170) REVERT: C 158 ASN cc_start: 0.8519 (m-40) cc_final: 0.8314 (m-40) REVERT: C 256 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: C 411 HIS cc_start: 0.7534 (t-90) cc_final: 0.7249 (t-90) REVERT: C 444 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8494 (ptp90) REVERT: C 607 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.9059 (p90) REVERT: C 610 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6898 (tp30) REVERT: C 622 ASP cc_start: 0.7619 (m-30) cc_final: 0.7346 (m-30) REVERT: D 93 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7557 (tpt-90) REVERT: D 95 ASP cc_start: 0.7497 (m-30) cc_final: 0.7212 (m-30) REVERT: D 256 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6304 (mp0) REVERT: D 397 PHE cc_start: 0.7923 (t80) cc_final: 0.7685 (t80) REVERT: D 567 MET cc_start: 0.7727 (mmm) cc_final: 0.7502 (mmt) REVERT: D 610 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6732 (tp30) REVERT: D 622 ASP cc_start: 0.7635 (m-30) cc_final: 0.7223 (m-30) REVERT: E 8 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7688 (pp) REVERT: E 93 ARG cc_start: 0.8063 (mmm160) cc_final: 0.7580 (tpt170) REVERT: E 158 ASN cc_start: 0.8518 (m-40) cc_final: 0.8314 (m-40) REVERT: E 256 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: E 444 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8484 (ptp90) REVERT: E 607 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.9061 (p90) REVERT: E 610 GLU cc_start: 0.7178 (mm-30) cc_final: 0.6904 (tp30) REVERT: E 622 ASP cc_start: 0.7616 (m-30) cc_final: 0.7344 (m-30) REVERT: F 93 ARG cc_start: 0.8030 (mmm160) cc_final: 0.7655 (tpt-90) REVERT: F 567 MET cc_start: 0.7788 (mmm) cc_final: 0.7538 (mmt) REVERT: F 607 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8911 (p90) REVERT: F 610 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6862 (tp30) outliers start: 88 outliers final: 59 residues processed: 342 average time/residue: 0.4174 time to fit residues: 233.0713 Evaluate side-chains 325 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 254 time to evaluate : 3.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 164 MET Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 403 LEU Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 242 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 367 optimal weight: 6.9990 chunk 308 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 chunk 244 optimal weight: 4.9990 chunk 271 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.111396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.090064 restraints weight = 125558.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.092613 restraints weight = 110839.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.093384 restraints weight = 77324.434| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 31320 Z= 0.295 Angle : 0.725 12.478 42516 Z= 0.372 Chirality : 0.047 0.189 4842 Planarity : 0.005 0.044 5580 Dihedral : 5.051 45.403 4358 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.33 % Allowed : 14.37 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.13), residues: 4062 helix: 0.82 (0.13), residues: 1452 sheet: 0.47 (0.18), residues: 762 loop : -0.52 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 172 HIS 0.008 0.002 HIS C 566 PHE 0.022 0.003 PHE A 595 TYR 0.025 0.003 TYR F 607 ARG 0.005 0.001 ARG C 580 Details of bonding type rmsd hydrogen bonds : bond 0.04339 ( 1344) hydrogen bonds : angle 5.18552 ( 3834) covalent geometry : bond 0.00696 (31320) covalent geometry : angle 0.72482 (42516) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 276 time to evaluate : 3.539 Fit side-chains REVERT: A 20 ARG cc_start: 0.6499 (mtt180) cc_final: 0.6282 (mtt-85) REVERT: A 93 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7639 (tpt-90) REVERT: A 95 ASP cc_start: 0.7473 (m-30) cc_final: 0.7079 (m-30) REVERT: A 256 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: A 610 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6956 (tp30) REVERT: B 93 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7739 (tpt-90) REVERT: B 567 MET cc_start: 0.7651 (mmm) cc_final: 0.7449 (mmt) REVERT: B 607 TYR cc_start: 0.9453 (OUTLIER) cc_final: 0.9099 (p90) REVERT: B 610 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7102 (tp30) REVERT: C 93 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7655 (tpt170) REVERT: C 158 ASN cc_start: 0.8662 (m-40) cc_final: 0.8418 (m-40) REVERT: C 287 MET cc_start: 0.8583 (tpp) cc_final: 0.8358 (mmm) REVERT: C 411 HIS cc_start: 0.7506 (t-90) cc_final: 0.7282 (t-90) REVERT: C 444 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8612 (ptp90) REVERT: C 610 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7029 (tp30) REVERT: D 20 ARG cc_start: 0.6499 (mtt180) cc_final: 0.6278 (mtt-85) REVERT: D 93 ARG cc_start: 0.8118 (mmm160) cc_final: 0.7638 (tpt-90) REVERT: D 95 ASP cc_start: 0.7471 (m-30) cc_final: 0.7082 (m-30) REVERT: D 256 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: D 567 MET cc_start: 0.7680 (mmm) cc_final: 0.7476 (mmt) REVERT: D 610 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7026 (tp30) REVERT: E 93 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7659 (tpt170) REVERT: E 158 ASN cc_start: 0.8661 (m-40) cc_final: 0.8423 (m-40) REVERT: E 287 MET cc_start: 0.8591 (tpp) cc_final: 0.8368 (mmm) REVERT: E 444 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8607 (ptp90) REVERT: E 610 GLU cc_start: 0.7388 (mm-30) cc_final: 0.6974 (tp30) REVERT: F 93 ARG cc_start: 0.8185 (mmm160) cc_final: 0.7740 (tpt-90) REVERT: F 607 TYR cc_start: 0.9450 (OUTLIER) cc_final: 0.9101 (p90) REVERT: F 610 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7097 (tp30) outliers start: 106 outliers final: 75 residues processed: 350 average time/residue: 0.4670 time to fit residues: 266.3456 Evaluate side-chains 336 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 255 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 615 ILE Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 273 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 373 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.115006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093214 restraints weight = 119367.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.094965 restraints weight = 83355.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095578 restraints weight = 78507.699| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31320 Z= 0.128 Angle : 0.583 10.327 42516 Z= 0.298 Chirality : 0.043 0.235 4842 Planarity : 0.004 0.037 5580 Dihedral : 4.648 42.974 4354 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.86 % Allowed : 14.78 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.13), residues: 4062 helix: 1.02 (0.14), residues: 1452 sheet: 0.61 (0.19), residues: 762 loop : -0.44 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 651 HIS 0.005 0.001 HIS F 74 PHE 0.025 0.002 PHE F 595 TYR 0.021 0.002 TYR C 607 ARG 0.004 0.000 ARG C 281 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 1344) hydrogen bonds : angle 4.86901 ( 3834) covalent geometry : bond 0.00302 (31320) covalent geometry : angle 0.58301 (42516) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 275 time to evaluate : 3.170 Fit side-chains REVERT: A 93 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7659 (tpt-90) REVERT: A 95 ASP cc_start: 0.7466 (m-30) cc_final: 0.7098 (m-30) REVERT: A 256 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: A 287 MET cc_start: 0.8716 (mmm) cc_final: 0.8492 (mmm) REVERT: A 397 PHE cc_start: 0.7948 (t80) cc_final: 0.7724 (t80) REVERT: A 610 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6809 (tp30) REVERT: B 93 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7392 (tpp80) REVERT: B 607 TYR cc_start: 0.9358 (OUTLIER) cc_final: 0.9096 (p90) REVERT: B 610 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6917 (tp30) REVERT: C 41 MET cc_start: 0.6610 (pmm) cc_final: 0.6230 (pmm) REVERT: C 93 ARG cc_start: 0.8199 (mmm160) cc_final: 0.7482 (tpt-90) REVERT: C 96 SER cc_start: 0.8605 (m) cc_final: 0.8071 (p) REVERT: C 166 GLU cc_start: 0.7737 (pp20) cc_final: 0.7533 (pp20) REVERT: C 256 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: C 444 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8462 (ptp90) REVERT: C 610 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6922 (tp30) REVERT: D 93 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7656 (tpt-90) REVERT: D 95 ASP cc_start: 0.7457 (m-30) cc_final: 0.7087 (m-30) REVERT: D 256 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: D 287 MET cc_start: 0.8730 (mmm) cc_final: 0.8502 (mmm) REVERT: D 397 PHE cc_start: 0.7952 (t80) cc_final: 0.7733 (t80) REVERT: D 610 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6860 (tp30) REVERT: E 41 MET cc_start: 0.6612 (pmm) cc_final: 0.6210 (pmm) REVERT: E 93 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7479 (tpt-90) REVERT: E 96 SER cc_start: 0.8599 (m) cc_final: 0.8072 (p) REVERT: E 166 GLU cc_start: 0.7732 (pp20) cc_final: 0.7520 (pp20) REVERT: E 256 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: E 444 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8444 (ptp90) REVERT: E 610 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6883 (tp30) REVERT: F 93 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7399 (tpp80) REVERT: F 607 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.9071 (p90) REVERT: F 610 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6891 (tp30) outliers start: 91 outliers final: 66 residues processed: 336 average time/residue: 0.3929 time to fit residues: 217.2214 Evaluate side-chains 325 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 251 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 111 optimal weight: 10.0000 chunk 206 optimal weight: 0.0870 chunk 185 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 346 optimal weight: 0.3980 chunk 263 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.115906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.093780 restraints weight = 112768.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095407 restraints weight = 70190.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095889 restraints weight = 71603.080| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31320 Z= 0.125 Angle : 0.577 12.528 42516 Z= 0.293 Chirality : 0.042 0.200 4842 Planarity : 0.004 0.035 5580 Dihedral : 4.468 43.022 4354 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.58 % Allowed : 15.44 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.13), residues: 4062 helix: 1.03 (0.14), residues: 1458 sheet: 0.75 (0.20), residues: 762 loop : -0.33 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 651 HIS 0.004 0.001 HIS F 74 PHE 0.025 0.002 PHE F 595 TYR 0.020 0.001 TYR B 607 ARG 0.004 0.000 ARG A 410 Details of bonding type rmsd hydrogen bonds : bond 0.03445 ( 1344) hydrogen bonds : angle 4.73925 ( 3834) covalent geometry : bond 0.00294 (31320) covalent geometry : angle 0.57698 (42516) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 283 time to evaluate : 3.193 Fit side-chains REVERT: A 41 MET cc_start: 0.6934 (pmm) cc_final: 0.6302 (pmm) REVERT: A 93 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7553 (tpt-90) REVERT: A 95 ASP cc_start: 0.7391 (m-30) cc_final: 0.7075 (m-30) REVERT: A 176 MET cc_start: 0.8409 (mtp) cc_final: 0.7982 (ttt) REVERT: A 239 MET cc_start: 0.8251 (tpp) cc_final: 0.7997 (tpp) REVERT: A 256 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: A 397 PHE cc_start: 0.7829 (t80) cc_final: 0.7567 (t80) REVERT: A 622 ASP cc_start: 0.7689 (m-30) cc_final: 0.7287 (m-30) REVERT: B 93 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7686 (tpt-90) REVERT: B 607 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.9075 (p90) REVERT: B 610 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6812 (tp30) REVERT: C 41 MET cc_start: 0.6745 (pmm) cc_final: 0.6327 (pmm) REVERT: C 76 LEU cc_start: 0.8294 (tp) cc_final: 0.8019 (tt) REVERT: C 93 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7457 (tpt-90) REVERT: C 96 SER cc_start: 0.8786 (m) cc_final: 0.8179 (p) REVERT: C 256 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: C 444 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8456 (ptp90) REVERT: C 567 MET cc_start: 0.7510 (mmm) cc_final: 0.7245 (mmt) REVERT: D 93 ARG cc_start: 0.7925 (mmm160) cc_final: 0.7553 (tpt-90) REVERT: D 95 ASP cc_start: 0.7377 (m-30) cc_final: 0.7065 (m-30) REVERT: D 176 MET cc_start: 0.8403 (mtp) cc_final: 0.7977 (ttt) REVERT: D 239 MET cc_start: 0.8244 (tpp) cc_final: 0.7990 (tpp) REVERT: D 256 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: D 397 PHE cc_start: 0.7834 (t80) cc_final: 0.7567 (t80) REVERT: D 610 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6866 (tp30) REVERT: D 622 ASP cc_start: 0.7696 (m-30) cc_final: 0.7327 (m-30) REVERT: E 41 MET cc_start: 0.6742 (pmm) cc_final: 0.6311 (pmm) REVERT: E 76 LEU cc_start: 0.8288 (tp) cc_final: 0.8019 (tt) REVERT: E 93 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7453 (tpt-90) REVERT: E 96 SER cc_start: 0.8783 (m) cc_final: 0.8176 (p) REVERT: E 256 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: E 444 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8466 (ptp90) REVERT: E 567 MET cc_start: 0.7460 (mmm) cc_final: 0.7213 (mmt) REVERT: F 93 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7694 (tpt-90) REVERT: F 607 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.9086 (p90) REVERT: F 610 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6827 (tp30) outliers start: 82 outliers final: 60 residues processed: 341 average time/residue: 0.3958 time to fit residues: 223.4108 Evaluate side-chains 327 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 3.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 132 optimal weight: 0.0370 chunk 140 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 375 optimal weight: 10.0000 chunk 206 optimal weight: 1.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.115710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.093999 restraints weight = 123585.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.096865 restraints weight = 97666.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097334 restraints weight = 76320.165| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31320 Z= 0.132 Angle : 0.591 12.422 42516 Z= 0.296 Chirality : 0.043 0.204 4842 Planarity : 0.004 0.035 5580 Dihedral : 4.419 43.652 4354 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.30 % Allowed : 16.10 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4062 helix: 0.96 (0.14), residues: 1494 sheet: 0.76 (0.20), residues: 762 loop : -0.33 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 162 HIS 0.007 0.001 HIS B 463 PHE 0.024 0.002 PHE B 595 TYR 0.020 0.001 TYR B 607 ARG 0.003 0.000 ARG E 281 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 1344) hydrogen bonds : angle 4.71553 ( 3834) covalent geometry : bond 0.00315 (31320) covalent geometry : angle 0.59071 (42516) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 265 time to evaluate : 3.660 Fit side-chains REVERT: A 41 MET cc_start: 0.7088 (pmm) cc_final: 0.6415 (pmm) REVERT: A 93 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7534 (tpt-90) REVERT: A 95 ASP cc_start: 0.7404 (m-30) cc_final: 0.7067 (m-30) REVERT: A 176 MET cc_start: 0.8406 (mtp) cc_final: 0.7998 (ttt) REVERT: A 239 MET cc_start: 0.8248 (tpp) cc_final: 0.7993 (tpp) REVERT: A 256 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: A 397 PHE cc_start: 0.7813 (t80) cc_final: 0.7610 (t80) REVERT: A 622 ASP cc_start: 0.7671 (m-30) cc_final: 0.7319 (m-30) REVERT: B 93 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7640 (tpt-90) REVERT: B 610 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6777 (tp30) REVERT: C 41 MET cc_start: 0.6816 (pmm) cc_final: 0.6246 (pmm) REVERT: C 76 LEU cc_start: 0.8333 (tp) cc_final: 0.8078 (tt) REVERT: C 93 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7508 (tpt170) REVERT: C 96 SER cc_start: 0.8717 (m) cc_final: 0.8149 (p) REVERT: C 256 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: C 444 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8480 (ptp90) REVERT: C 567 MET cc_start: 0.7514 (mmm) cc_final: 0.7275 (mmt) REVERT: D 93 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7534 (tpt-90) REVERT: D 95 ASP cc_start: 0.7395 (m-30) cc_final: 0.7058 (m-30) REVERT: D 176 MET cc_start: 0.8406 (mtp) cc_final: 0.8004 (ttt) REVERT: D 239 MET cc_start: 0.8234 (tpp) cc_final: 0.7984 (tpp) REVERT: D 256 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: D 397 PHE cc_start: 0.7812 (t80) cc_final: 0.7605 (t80) REVERT: D 610 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6936 (tp30) REVERT: D 622 ASP cc_start: 0.7717 (m-30) cc_final: 0.7335 (m-30) REVERT: E 41 MET cc_start: 0.6807 (pmm) cc_final: 0.6218 (pmm) REVERT: E 76 LEU cc_start: 0.8328 (tp) cc_final: 0.8074 (tt) REVERT: E 93 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7507 (tpt170) REVERT: E 96 SER cc_start: 0.8707 (m) cc_final: 0.8141 (p) REVERT: E 256 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: E 444 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8467 (ptp90) REVERT: E 567 MET cc_start: 0.7528 (mmm) cc_final: 0.7287 (mmt) REVERT: F 93 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7645 (tpt-90) REVERT: F 610 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6791 (tp30) outliers start: 73 outliers final: 61 residues processed: 311 average time/residue: 0.6223 time to fit residues: 326.8596 Evaluate side-chains 320 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 253 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 161 CYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 161 CYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 198 optimal weight: 7.9990 chunk 281 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 338 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 332 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 373 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 372 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 583 HIS C 158 ASN C 583 HIS ** D 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 583 HIS ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.088272 restraints weight = 120805.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090727 restraints weight = 108863.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091366 restraints weight = 77620.634| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 31320 Z= 0.392 Angle : 0.840 14.339 42516 Z= 0.429 Chirality : 0.051 0.223 4842 Planarity : 0.006 0.060 5580 Dihedral : 5.178 19.322 4350 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.64 % Allowed : 16.07 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4062 helix: 0.41 (0.13), residues: 1452 sheet: -0.03 (0.19), residues: 762 loop : -0.73 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 12 HIS 0.009 0.002 HIS E 492 PHE 0.024 0.003 PHE C 656 TYR 0.026 0.003 TYR D 607 ARG 0.006 0.001 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.04825 ( 1344) hydrogen bonds : angle 5.53959 ( 3834) covalent geometry : bond 0.00932 (31320) covalent geometry : angle 0.83976 (42516) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 247 time to evaluate : 3.220 Fit side-chains REVERT: A 41 MET cc_start: 0.7356 (pmm) cc_final: 0.6568 (pmm) REVERT: A 93 ARG cc_start: 0.8259 (mmm160) cc_final: 0.7660 (tpt-90) REVERT: A 95 ASP cc_start: 0.7344 (m-30) cc_final: 0.6925 (m-30) REVERT: A 239 MET cc_start: 0.8392 (tpp) cc_final: 0.8186 (tpp) REVERT: A 256 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: A 434 ILE cc_start: 0.7760 (mt) cc_final: 0.7558 (mp) REVERT: B 93 ARG cc_start: 0.8252 (mmm160) cc_final: 0.7600 (tpt-90) REVERT: B 607 TYR cc_start: 0.9365 (OUTLIER) cc_final: 0.8867 (p90) REVERT: B 610 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7039 (tp30) REVERT: C 76 LEU cc_start: 0.8415 (tp) cc_final: 0.8190 (tt) REVERT: C 93 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7632 (tpt-90) REVERT: C 211 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8827 (tt) REVERT: C 324 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8344 (t) REVERT: C 334 MET cc_start: 0.8008 (ttp) cc_final: 0.7548 (ttm) REVERT: C 444 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8600 (ptp90) REVERT: C 567 MET cc_start: 0.7492 (mmm) cc_final: 0.7266 (mmt) REVERT: C 607 TYR cc_start: 0.9413 (OUTLIER) cc_final: 0.9076 (p90) REVERT: C 610 GLU cc_start: 0.7554 (tp30) cc_final: 0.7138 (tp30) REVERT: D 93 ARG cc_start: 0.8263 (mmm160) cc_final: 0.7664 (tpt-90) REVERT: D 95 ASP cc_start: 0.7350 (m-30) cc_final: 0.6924 (m-30) REVERT: D 239 MET cc_start: 0.8373 (tpp) cc_final: 0.8167 (tpp) REVERT: D 256 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6568 (mp0) REVERT: D 610 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6968 (tp30) REVERT: E 76 LEU cc_start: 0.8413 (tp) cc_final: 0.8191 (tt) REVERT: E 93 ARG cc_start: 0.8236 (mmm160) cc_final: 0.7634 (tpt-90) REVERT: E 211 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8830 (tt) REVERT: E 444 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8591 (ptp90) REVERT: E 567 MET cc_start: 0.7511 (mmm) cc_final: 0.7267 (mmt) REVERT: E 607 TYR cc_start: 0.9438 (OUTLIER) cc_final: 0.9090 (p90) REVERT: E 610 GLU cc_start: 0.7599 (tp30) cc_final: 0.7182 (tp30) REVERT: F 93 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7604 (tpt-90) REVERT: F 607 TYR cc_start: 0.9367 (OUTLIER) cc_final: 0.8854 (p90) REVERT: F 610 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7043 (tp30) outliers start: 84 outliers final: 64 residues processed: 306 average time/residue: 0.3991 time to fit residues: 201.7513 Evaluate side-chains 307 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 232 time to evaluate : 3.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 607 TYR Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 161 CYS Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 607 TYR Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 161 CYS Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 607 TYR Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 98 optimal weight: 0.8980 chunk 320 optimal weight: 0.7980 chunk 251 optimal weight: 0.6980 chunk 204 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 chunk 400 optimal weight: 0.9980 chunk 234 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 266 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.114452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092639 restraints weight = 125199.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.095557 restraints weight = 97165.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095990 restraints weight = 75982.287| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31320 Z= 0.136 Angle : 0.620 13.042 42516 Z= 0.314 Chirality : 0.044 0.220 4842 Planarity : 0.004 0.038 5580 Dihedral : 4.640 18.062 4350 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.92 % Allowed : 17.17 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 4062 helix: 0.77 (0.14), residues: 1458 sheet: 0.20 (0.20), residues: 768 loop : -0.48 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 162 HIS 0.008 0.001 HIS A 463 PHE 0.024 0.002 PHE B 595 TYR 0.017 0.002 TYR E 607 ARG 0.004 0.000 ARG A 241 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1344) hydrogen bonds : angle 4.99425 ( 3834) covalent geometry : bond 0.00320 (31320) covalent geometry : angle 0.61954 (42516) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 268 time to evaluate : 3.209 Fit side-chains REVERT: A 41 MET cc_start: 0.7325 (pmm) cc_final: 0.6546 (pmm) REVERT: A 93 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7609 (tpt-90) REVERT: A 95 ASP cc_start: 0.7309 (m-30) cc_final: 0.6919 (m-30) REVERT: A 256 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6452 (mp0) REVERT: A 397 PHE cc_start: 0.7859 (t80) cc_final: 0.7633 (t80) REVERT: B 93 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7651 (tpt-90) REVERT: B 610 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6845 (tp30) REVERT: C 76 LEU cc_start: 0.8302 (tp) cc_final: 0.8057 (tt) REVERT: C 93 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7506 (tpt-90) REVERT: C 96 SER cc_start: 0.8644 (m) cc_final: 0.8072 (p) REVERT: C 211 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8645 (tt) REVERT: C 324 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8305 (t) REVERT: C 567 MET cc_start: 0.7425 (mmm) cc_final: 0.7199 (mmt) REVERT: D 41 MET cc_start: 0.7122 (pmm) cc_final: 0.6526 (pmm) REVERT: D 93 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7596 (tpt-90) REVERT: D 256 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6447 (mp0) REVERT: D 397 PHE cc_start: 0.7863 (t80) cc_final: 0.7596 (t80) REVERT: D 567 MET cc_start: 0.7553 (mmm) cc_final: 0.7349 (mmt) REVERT: E 76 LEU cc_start: 0.8294 (tp) cc_final: 0.8041 (tt) REVERT: E 93 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7498 (tpt-90) REVERT: E 96 SER cc_start: 0.8647 (m) cc_final: 0.8076 (p) REVERT: E 211 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8653 (tt) REVERT: E 324 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8312 (t) REVERT: E 444 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8586 (ptp90) REVERT: E 567 MET cc_start: 0.7414 (mmm) cc_final: 0.7189 (mmt) REVERT: F 93 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7382 (tpp80) REVERT: F 567 MET cc_start: 0.7561 (mmm) cc_final: 0.7348 (mmt) REVERT: F 610 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6888 (tp30) outliers start: 61 outliers final: 50 residues processed: 306 average time/residue: 0.4344 time to fit residues: 220.0988 Evaluate side-chains 315 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 3.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 256 GLU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 522 ASP Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 404 MET Chi-restraints excluded: chain C residue 522 ASP Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 540 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 444 ARG Chi-restraints excluded: chain E residue 522 ASP Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 404 MET Chi-restraints excluded: chain F residue 522 ASP Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 63 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 345 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 331 optimal weight: 10.0000 chunk 268 optimal weight: 10.0000 chunk 340 optimal weight: 0.5980 chunk 113 optimal weight: 0.0040 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.114917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.093050 restraints weight = 123196.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095755 restraints weight = 91551.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.096117 restraints weight = 77052.049| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31320 Z= 0.137 Angle : 0.605 13.423 42516 Z= 0.304 Chirality : 0.043 0.230 4842 Planarity : 0.004 0.033 5580 Dihedral : 4.440 17.601 4350 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.73 % Allowed : 17.36 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.13), residues: 4062 helix: 0.91 (0.14), residues: 1458 sheet: 0.32 (0.20), residues: 768 loop : -0.38 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 162 HIS 0.006 0.001 HIS B 463 PHE 0.024 0.002 PHE D 595 TYR 0.018 0.001 TYR C 607 ARG 0.003 0.000 ARG E 281 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1344) hydrogen bonds : angle 4.84732 ( 3834) covalent geometry : bond 0.00327 (31320) covalent geometry : angle 0.60469 (42516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10061.12 seconds wall clock time: 176 minutes 45.53 seconds (10605.53 seconds total)