Starting phenix.real_space_refine on Wed May 28 12:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvi_17967/05_2025/8pvi_17967.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvi_17967/05_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_17967/05_2025/8pvi_17967.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvi_17967/05_2025/8pvi_17967.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvi_17967/05_2025/8pvi_17967.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvi_17967/05_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-5687/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: 16.42, per 1000 atoms: 0.53 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: 7.19 Conformation dependent library (CDL) restraints added in 7.7 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: 4.70 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: 13.15 Time building geometry restraints manager: 8.76 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: 0.25 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: 2.980 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: 0.040 Extract box with map and model: 1.350 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 73.490 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.830 ------------------------------------------------------------------------------- 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 : 3.330 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: 0.4642 time to fit residues: 561.7390 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 : 3.051 ------------------------------------------------------------------------------- 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 = 0.3259 r_free = 0.3259 target = 0.092669 restraints weight = 101524.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094280 restraints weight = 64726.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095039 restraints weight = 53652.105| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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 = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 0.70683 (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 : 3.708 Fit side-chains REVERT: A 93 ARG cc_start: 0.7943 (mmm160) cc_final: 0.7532 (tpt-90) REVERT: A 256 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6344 (mp0) REVERT: A 610 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6912 (tp30) REVERT: A 622 ASP cc_start: 0.7658 (m-30) cc_final: 0.7252 (m-30) REVERT: B 93 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7547 (tpt-90) REVERT: B 158 ASN cc_start: 0.8349 (m-40) cc_final: 0.8117 (m-40) REVERT: B 256 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: B 293 GLN cc_start: 0.7178 (mt0) cc_final: 0.6817 (mt0) REVERT: B 411 HIS cc_start: 0.7589 (t-90) cc_final: 0.7082 (t-90) REVERT: B 607 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8926 (p90) REVERT: B 610 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6981 (tp30) REVERT: C 93 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7458 (tpt170) REVERT: C 158 ASN cc_start: 0.8428 (m-40) cc_final: 0.8123 (m-40) REVERT: C 164 MET cc_start: 0.7198 (ttp) cc_final: 0.6912 (ttt) REVERT: C 293 GLN cc_start: 0.7248 (mt0) cc_final: 0.6931 (mt0) REVERT: C 411 HIS cc_start: 0.7617 (t-90) cc_final: 0.7110 (t-90) REVERT: C 567 MET cc_start: 0.7719 (mmm) cc_final: 0.7513 (mmt) REVERT: C 607 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.9107 (p90) REVERT: C 610 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6957 (tp30) REVERT: C 622 ASP cc_start: 0.7723 (m-30) cc_final: 0.7522 (m-30) REVERT: D 93 ARG cc_start: 0.7944 (mmm160) cc_final: 0.7531 (tpt-90) REVERT: D 256 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: D 610 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6913 (tp30) REVERT: D 622 ASP cc_start: 0.7661 (m-30) cc_final: 0.7244 (m-30) REVERT: E 93 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7460 (tpt170) REVERT: E 158 ASN cc_start: 0.8433 (m-40) cc_final: 0.8129 (m-40) REVERT: E 164 MET cc_start: 0.7186 (ttp) cc_final: 0.6898 (ttt) REVERT: E 293 GLN cc_start: 0.7233 (mt0) cc_final: 0.6927 (mt0) REVERT: E 411 HIS cc_start: 0.7612 (t-90) cc_final: 0.7111 (t-90) REVERT: E 567 MET cc_start: 0.7711 (mmm) cc_final: 0.7510 (mmt) REVERT: E 607 TYR cc_start: 0.9377 (OUTLIER) cc_final: 0.9106 (p90) REVERT: E 610 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6956 (tp30) REVERT: E 622 ASP cc_start: 0.7716 (m-30) cc_final: 0.7511 (m-30) REVERT: F 93 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7551 (tpt-90) REVERT: F 158 ASN cc_start: 0.8341 (m-40) cc_final: 0.8117 (m-40) REVERT: F 256 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: F 293 GLN cc_start: 0.7175 (mt0) cc_final: 0.6810 (mt0) REVERT: F 411 HIS cc_start: 0.7608 (t-90) cc_final: 0.7087 (t-90) REVERT: F 607 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.8927 (p90) REVERT: F 610 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6992 (tp30) outliers start: 104 outliers final: 42 residues processed: 458 average time/residue: 0.4364 time to fit residues: 319.5311 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 : 3.349 ------------------------------------------------------------------------------- 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: 7.9990 chunk 97 optimal weight: 0.6980 chunk 268 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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** B 414 GLN 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** F 414 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095146 restraints weight = 92414.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.095209 restraints weight = 64515.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096532 restraints weight = 55644.520| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31320 Z= 0.130 Angle : 0.591 12.004 42516 Z= 0.306 Chirality : 0.043 0.215 4842 Planarity : 0.004 0.034 5580 Dihedral : 4.694 40.005 4358 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.14 % Allowed : 13.71 % Favored : 84.15 % 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: 0.73 (0.13), residues: 4062 helix: 1.32 (0.13), residues: 1446 sheet: 0.91 (0.19), residues: 786 loop : -0.33 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 12 HIS 0.004 0.001 HIS C 463 PHE 0.026 0.002 PHE E 595 TYR 0.021 0.002 TYR B 607 ARG 0.005 0.001 ARG E 281 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 1344) hydrogen bonds : angle 4.86748 ( 3834) covalent geometry : bond 0.00294 (31320) covalent geometry : angle 0.59137 (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 406 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 338 time to evaluate : 3.175 Fit side-chains REVERT: A 93 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7587 (tpt-90) REVERT: A 95 ASP cc_start: 0.7527 (m-30) cc_final: 0.7266 (m-30) REVERT: A 256 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: A 567 MET cc_start: 0.7680 (mmm) cc_final: 0.7176 (mmt) REVERT: A 610 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6783 (tp30) REVERT: A 622 ASP cc_start: 0.7464 (m-30) cc_final: 0.7191 (m-30) REVERT: B 93 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7614 (tpt-90) REVERT: B 607 TYR cc_start: 0.9281 (OUTLIER) cc_final: 0.8838 (p90) REVERT: B 610 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6859 (tp30) REVERT: C 8 LEU cc_start: 0.7786 (pp) cc_final: 0.7490 (pp) REVERT: C 93 ARG cc_start: 0.8003 (mmm160) cc_final: 0.7726 (tpt-90) REVERT: C 158 ASN cc_start: 0.8481 (m-40) cc_final: 0.8154 (m-40) REVERT: C 176 MET cc_start: 0.8400 (mtp) cc_final: 0.8097 (ttt) REVERT: C 256 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6283 (mp0) REVERT: C 411 HIS cc_start: 0.7544 (t-90) cc_final: 0.7001 (t-90) REVERT: C 607 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.8985 (p90) REVERT: C 610 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6863 (tp30) REVERT: C 622 ASP cc_start: 0.7581 (m-30) cc_final: 0.7356 (m-30) REVERT: D 93 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7580 (tpt-90) REVERT: D 95 ASP cc_start: 0.7512 (m-30) cc_final: 0.7253 (m-30) REVERT: D 256 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: D 567 MET cc_start: 0.7692 (mmm) cc_final: 0.7176 (mmt) REVERT: D 610 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6791 (tp30) REVERT: D 622 ASP cc_start: 0.7458 (m-30) cc_final: 0.7182 (m-30) REVERT: E 8 LEU cc_start: 0.7791 (pp) cc_final: 0.7494 (pp) REVERT: E 93 ARG cc_start: 0.8010 (mmm160) cc_final: 0.7731 (tpt-90) REVERT: E 158 ASN cc_start: 0.8467 (m-40) cc_final: 0.8154 (m-40) REVERT: E 176 MET cc_start: 0.8404 (mtp) cc_final: 0.8103 (ttt) REVERT: E 256 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: E 411 HIS cc_start: 0.7538 (t-90) cc_final: 0.7013 (t-90) REVERT: E 607 TYR cc_start: 0.9304 (OUTLIER) cc_final: 0.8991 (p90) REVERT: E 610 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6838 (tp30) REVERT: E 622 ASP cc_start: 0.7567 (m-30) cc_final: 0.7343 (m-30) REVERT: F 93 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7618 (tpt-90) REVERT: F 607 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8841 (p90) REVERT: F 610 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6867 (tp30) outliers start: 68 outliers final: 34 residues processed: 382 average time/residue: 0.4173 time to fit residues: 255.5480 Evaluate side-chains 310 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 3.124 ------------------------------------------------------------------------------- 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 670 THR Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 227 VAL 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 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 670 THR 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 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 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: 0.9990 chunk 224 optimal weight: 2.9990 chunk 389 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 314 optimal weight: 0.6980 chunk 365 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 397 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 392 HIS ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 HIS C 273 GLN ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 GLN D 392 HIS E 74 HIS E 273 GLN ** 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** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093483 restraints weight = 92583.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093621 restraints weight = 65383.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094886 restraints weight = 55006.003| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 31320 Z= 0.152 Angle : 0.593 10.398 42516 Z= 0.305 Chirality : 0.043 0.192 4842 Planarity : 0.004 0.035 5580 Dihedral : 4.652 41.119 4358 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.70 % Allowed : 14.56 % Favored : 82.74 % 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: 0.60 (0.13), residues: 4062 helix: 1.10 (0.13), residues: 1488 sheet: 0.93 (0.18), residues: 780 loop : -0.37 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 172 HIS 0.004 0.001 HIS F 74 PHE 0.023 0.002 PHE A 595 TYR 0.023 0.002 TYR C 607 ARG 0.003 0.000 ARG C 580 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1344) hydrogen bonds : angle 4.78854 ( 3834) covalent geometry : bond 0.00353 (31320) covalent geometry : angle 0.59305 (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 361 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 275 time to evaluate : 3.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7557 (tpt-90) REVERT: A 95 ASP cc_start: 0.7463 (m-30) cc_final: 0.7158 (m-30) REVERT: A 256 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6318 (mp0) REVERT: A 567 MET cc_start: 0.7701 (mmm) cc_final: 0.7306 (mmt) REVERT: A 610 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6714 (tp30) REVERT: A 622 ASP cc_start: 0.7644 (m-30) cc_final: 0.7225 (m-30) REVERT: B 93 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7609 (tpt-90) REVERT: B 567 MET cc_start: 0.7837 (mmm) cc_final: 0.7557 (mmt) REVERT: B 607 TYR cc_start: 0.9297 (OUTLIER) cc_final: 0.8973 (p90) REVERT: B 610 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6863 (tp30) REVERT: C 93 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7562 (tpt170) REVERT: C 158 ASN cc_start: 0.8545 (m-40) cc_final: 0.8339 (m-40) REVERT: C 256 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: C 411 HIS cc_start: 0.7565 (t-90) cc_final: 0.7238 (t-90) REVERT: C 444 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8503 (ptp90) REVERT: C 607 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.9054 (p90) REVERT: C 610 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6895 (tp30) REVERT: C 622 ASP cc_start: 0.7593 (m-30) cc_final: 0.7351 (m-30) REVERT: D 93 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7553 (tpt-90) REVERT: D 95 ASP cc_start: 0.7448 (m-30) cc_final: 0.7152 (m-30) REVERT: D 256 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: D 567 MET cc_start: 0.7726 (mmm) cc_final: 0.7326 (mmt) REVERT: D 610 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6719 (tp30) REVERT: D 622 ASP cc_start: 0.7637 (m-30) cc_final: 0.7219 (m-30) REVERT: E 93 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7563 (tpt170) REVERT: E 158 ASN cc_start: 0.8543 (m-40) cc_final: 0.8338 (m-40) REVERT: E 256 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6443 (mp0) REVERT: E 411 HIS cc_start: 0.7567 (t-90) cc_final: 0.7265 (t-90) REVERT: E 444 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8497 (ptp90) REVERT: E 607 TYR cc_start: 0.9324 (OUTLIER) cc_final: 0.9056 (p90) REVERT: E 610 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6894 (tp30) REVERT: E 622 ASP cc_start: 0.7590 (m-30) cc_final: 0.7345 (m-30) REVERT: F 93 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7616 (tpt-90) REVERT: F 567 MET cc_start: 0.7828 (mmm) cc_final: 0.7543 (mmt) REVERT: F 607 TYR cc_start: 0.9307 (OUTLIER) cc_final: 0.8979 (p90) REVERT: F 610 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6868 (tp30) outliers start: 86 outliers final: 61 residues processed: 335 average time/residue: 0.4043 time to fit residues: 219.2271 Evaluate side-chains 323 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 252 time to evaluate : 3.532 ------------------------------------------------------------------------------- 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 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 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 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 428 VAL 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: 0.0980 chunk 274 optimal weight: 5.9990 chunk 367 optimal weight: 0.9990 chunk 308 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 chunk 244 optimal weight: 0.9980 chunk 271 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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 273 GLN ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN E 273 GLN ** E 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.115636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.093796 restraints weight = 125512.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.096658 restraints weight = 97139.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097078 restraints weight = 76051.698| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31320 Z= 0.144 Angle : 0.592 12.211 42516 Z= 0.300 Chirality : 0.043 0.206 4842 Planarity : 0.004 0.038 5580 Dihedral : 4.583 41.614 4358 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.80 % Allowed : 14.91 % 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: 0.61 (0.13), residues: 4062 helix: 1.06 (0.13), residues: 1488 sheet: 0.95 (0.19), residues: 780 loop : -0.33 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 162 HIS 0.004 0.001 HIS E 566 PHE 0.024 0.002 PHE D 595 TYR 0.022 0.002 TYR F 607 ARG 0.003 0.000 ARG C 580 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1344) hydrogen bonds : angle 4.73949 ( 3834) covalent geometry : bond 0.00339 (31320) covalent geometry : angle 0.59167 (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 364 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 275 time to evaluate : 3.107 Fit side-chains REVERT: A 93 ARG cc_start: 0.7920 (mmm160) cc_final: 0.7576 (tpt-90) REVERT: A 95 ASP cc_start: 0.7488 (m-30) cc_final: 0.7179 (m-30) REVERT: A 256 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: A 301 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8606 (mt) REVERT: A 397 PHE cc_start: 0.7988 (t80) cc_final: 0.7747 (t80) REVERT: A 567 MET cc_start: 0.7708 (mmm) cc_final: 0.7488 (mmt) REVERT: A 610 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6855 (tp30) REVERT: A 622 ASP cc_start: 0.7675 (m-30) cc_final: 0.7220 (m-30) REVERT: B 93 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7671 (tpt-90) REVERT: B 567 MET cc_start: 0.7701 (mmm) cc_final: 0.7451 (mmt) REVERT: B 607 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.8994 (p90) REVERT: B 610 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6839 (tp30) REVERT: C 93 ARG cc_start: 0.8089 (mmm160) cc_final: 0.7571 (tpt170) REVERT: C 96 SER cc_start: 0.8663 (m) cc_final: 0.7987 (p) REVERT: C 158 ASN cc_start: 0.8590 (m-40) cc_final: 0.8383 (m-40) REVERT: C 256 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: C 411 HIS cc_start: 0.7430 (t-90) cc_final: 0.7164 (t-90) REVERT: C 444 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8491 (ptp90) REVERT: C 607 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.9016 (p90) REVERT: C 610 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7013 (tp30) REVERT: D 93 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7572 (tpt-90) REVERT: D 95 ASP cc_start: 0.7485 (m-30) cc_final: 0.7179 (m-30) REVERT: D 256 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6386 (mp0) REVERT: D 301 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8610 (mt) REVERT: D 397 PHE cc_start: 0.7983 (t80) cc_final: 0.7749 (t80) REVERT: D 567 MET cc_start: 0.7692 (mmm) cc_final: 0.7471 (mmt) REVERT: D 610 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6881 (tp30) REVERT: D 622 ASP cc_start: 0.7712 (m-30) cc_final: 0.7275 (m-30) REVERT: E 93 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7562 (tpt170) REVERT: E 96 SER cc_start: 0.8662 (m) cc_final: 0.7985 (p) REVERT: E 158 ASN cc_start: 0.8591 (m-40) cc_final: 0.8382 (m-40) REVERT: E 256 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6626 (mp0) REVERT: E 411 HIS cc_start: 0.7430 (t-90) cc_final: 0.7161 (t-90) REVERT: E 444 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8483 (ptp90) REVERT: E 607 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.9106 (p90) REVERT: E 610 GLU cc_start: 0.7254 (mm-30) cc_final: 0.7031 (tp30) REVERT: F 93 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7672 (tpt-90) REVERT: F 567 MET cc_start: 0.7789 (mmm) cc_final: 0.7522 (mmt) REVERT: F 607 TYR cc_start: 0.9378 (OUTLIER) cc_final: 0.9020 (p90) REVERT: F 610 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6829 (tp30) outliers start: 89 outliers final: 60 residues processed: 337 average time/residue: 0.4095 time to fit residues: 226.5987 Evaluate side-chains 325 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 253 time to evaluate : 3.490 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 428 VAL 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 663 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 273 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 chunk 373 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 450 GLN E 450 GLN ** 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 = 0.3577 r_free = 0.3577 target = 0.112948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.091248 restraints weight = 125064.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094242 restraints weight = 100039.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.094695 restraints weight = 74369.115| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 31320 Z= 0.221 Angle : 0.642 9.180 42516 Z= 0.331 Chirality : 0.045 0.221 4842 Planarity : 0.005 0.043 5580 Dihedral : 4.826 44.672 4358 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.27 % Allowed : 14.59 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.13), residues: 4062 helix: 0.90 (0.14), residues: 1452 sheet: 0.72 (0.19), residues: 762 loop : -0.41 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 162 HIS 0.005 0.001 HIS D 492 PHE 0.022 0.002 PHE A 595 TYR 0.025 0.002 TYR F 607 ARG 0.005 0.001 ARG E 281 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 1344) hydrogen bonds : angle 4.96749 ( 3834) covalent geometry : bond 0.00522 (31320) covalent geometry : angle 0.64189 (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 388 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 284 time to evaluate : 3.185 Fit side-chains REVERT: A 20 ARG cc_start: 0.6534 (mtt180) cc_final: 0.6330 (mtt-85) REVERT: A 93 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7610 (tpt-90) REVERT: A 95 ASP cc_start: 0.7430 (m-30) cc_final: 0.7051 (m-30) REVERT: A 256 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: A 397 PHE cc_start: 0.8058 (t80) cc_final: 0.7666 (t80) REVERT: A 610 GLU cc_start: 0.7213 (mm-30) cc_final: 0.6850 (tp30) REVERT: B 93 ARG cc_start: 0.8141 (mmm160) cc_final: 0.7666 (tpt-90) REVERT: B 263 CYS cc_start: 0.7881 (t) cc_final: 0.7676 (t) REVERT: B 567 MET cc_start: 0.7657 (mmm) cc_final: 0.7437 (mmt) REVERT: B 607 TYR cc_start: 0.9407 (OUTLIER) cc_final: 0.9099 (p90) REVERT: B 610 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6958 (tp30) REVERT: C 41 MET cc_start: 0.6743 (pmm) cc_final: 0.6390 (pmm) REVERT: C 93 ARG cc_start: 0.8215 (mmm160) cc_final: 0.7469 (tpt-90) REVERT: C 96 SER cc_start: 0.8599 (m) cc_final: 0.8012 (p) REVERT: C 256 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: C 411 HIS cc_start: 0.7474 (t-90) cc_final: 0.7241 (t-90) REVERT: C 444 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8497 (ptp90) REVERT: C 567 MET cc_start: 0.7606 (mmm) cc_final: 0.7343 (mmt) REVERT: C 610 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7016 (tp30) REVERT: D 20 ARG cc_start: 0.6533 (mtt180) cc_final: 0.6327 (mtt-85) REVERT: D 93 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7604 (tpt-90) REVERT: D 95 ASP cc_start: 0.7431 (m-30) cc_final: 0.7052 (m-30) REVERT: D 256 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: D 397 PHE cc_start: 0.8052 (t80) cc_final: 0.7661 (t80) REVERT: D 610 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6902 (tp30) REVERT: E 41 MET cc_start: 0.6748 (pmm) cc_final: 0.6380 (pmm) REVERT: E 93 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7466 (tpt-90) REVERT: E 96 SER cc_start: 0.8593 (m) cc_final: 0.8005 (p) REVERT: E 256 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: E 411 HIS cc_start: 0.7481 (t-90) cc_final: 0.7243 (t-90) REVERT: E 444 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8480 (ptp90) REVERT: E 567 MET cc_start: 0.7633 (mmm) cc_final: 0.7372 (mmt) REVERT: E 610 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6979 (tp30) REVERT: F 93 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7668 (tpt-90) REVERT: F 263 CYS cc_start: 0.7898 (t) cc_final: 0.7684 (t) REVERT: F 567 MET cc_start: 0.7681 (mmm) cc_final: 0.7456 (mmt) REVERT: F 607 TYR cc_start: 0.9405 (OUTLIER) cc_final: 0.9085 (p90) REVERT: F 610 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6922 (tp30) outliers start: 104 outliers final: 67 residues processed: 352 average time/residue: 0.3909 time to fit residues: 224.8335 Evaluate side-chains 330 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 255 time to evaluate : 3.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 324 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 MET 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 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 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 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 211 ILE 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 404 MET 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 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 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 403 LEU 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 615 ILE 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: 6.9990 chunk 206 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 358 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 365 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** 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 = 0.3594 r_free = 0.3594 target = 0.113956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.092146 restraints weight = 114017.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.093368 restraints weight = 77225.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.093964 restraints weight = 80201.902| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31320 Z= 0.171 Angle : 0.608 12.554 42516 Z= 0.311 Chirality : 0.044 0.200 4842 Planarity : 0.004 0.040 5580 Dihedral : 4.655 44.031 4354 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.89 % Allowed : 15.41 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.14), residues: 1452 sheet: 0.65 (0.19), residues: 762 loop : -0.41 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 162 HIS 0.005 0.001 HIS F 74 PHE 0.024 0.002 PHE A 595 TYR 0.023 0.002 TYR F 607 ARG 0.004 0.000 ARG C 281 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 1344) hydrogen bonds : angle 4.89950 ( 3834) covalent geometry : bond 0.00405 (31320) covalent geometry : angle 0.60829 (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 370 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 278 time to evaluate : 3.153 Fit side-chains REVERT: A 93 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7664 (tpt-90) REVERT: A 95 ASP cc_start: 0.7440 (m-30) cc_final: 0.7076 (m-30) REVERT: A 239 MET cc_start: 0.8267 (tpp) cc_final: 0.8028 (tpp) REVERT: A 256 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: A 397 PHE cc_start: 0.7936 (t80) cc_final: 0.7673 (t80) REVERT: A 610 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6787 (tp30) REVERT: B 93 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7416 (tpp80) REVERT: B 607 TYR cc_start: 0.9387 (OUTLIER) cc_final: 0.9127 (p90) REVERT: B 610 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6956 (tp30) REVERT: C 41 MET cc_start: 0.6782 (pmm) cc_final: 0.6223 (pmm) REVERT: C 76 LEU cc_start: 0.8302 (tp) cc_final: 0.8029 (tt) REVERT: C 93 ARG cc_start: 0.8214 (mmm160) cc_final: 0.7552 (tpt-90) REVERT: C 256 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: C 324 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8185 (t) REVERT: C 444 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8511 (ptp90) REVERT: C 567 MET cc_start: 0.7584 (mmm) cc_final: 0.7339 (mmt) REVERT: C 610 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6863 (tp30) REVERT: D 93 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7664 (tpt-90) REVERT: D 95 ASP cc_start: 0.7427 (m-30) cc_final: 0.7041 (m-30) REVERT: D 239 MET cc_start: 0.8250 (tpp) cc_final: 0.8011 (tpp) REVERT: D 256 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6402 (mp0) REVERT: D 397 PHE cc_start: 0.7931 (t80) cc_final: 0.7674 (t80) REVERT: D 610 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6812 (tp30) REVERT: E 41 MET cc_start: 0.6780 (pmm) cc_final: 0.6216 (pmm) REVERT: E 76 LEU cc_start: 0.8292 (tp) cc_final: 0.8026 (tt) REVERT: E 93 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7548 (tpt-90) REVERT: E 256 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: E 324 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8189 (t) REVERT: E 444 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8503 (ptp90) REVERT: E 567 MET cc_start: 0.7608 (mmm) cc_final: 0.7367 (mmt) REVERT: E 610 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6866 (tp30) REVERT: F 93 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7420 (tpp80) REVERT: F 567 MET cc_start: 0.7547 (mmm) cc_final: 0.7341 (mmt) REVERT: F 607 TYR cc_start: 0.9370 (OUTLIER) cc_final: 0.9090 (p90) REVERT: F 610 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6876 (tp30) outliers start: 92 outliers final: 69 residues processed: 337 average time/residue: 0.3954 time to fit residues: 219.2894 Evaluate side-chains 339 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 260 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 607 TYR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 616 GLU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 8 LEU 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 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 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 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 428 VAL 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 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 403 LEU 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 615 ILE Chi-restraints excluded: chain F residue 616 GLU 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: 2.9990 chunk 140 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 217 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 375 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3586 r_free = 0.3586 target = 0.113425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.091942 restraints weight = 125428.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.093722 restraints weight = 118599.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095168 restraints weight = 79951.929| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31320 Z= 0.182 Angle : 0.607 12.311 42516 Z= 0.312 Chirality : 0.044 0.213 4842 Planarity : 0.004 0.042 5580 Dihedral : 4.673 45.102 4354 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.67 % Allowed : 15.85 % Favored : 81.48 % 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: 0.28 (0.13), residues: 4062 helix: 0.85 (0.14), residues: 1458 sheet: 0.53 (0.20), residues: 762 loop : -0.41 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 162 HIS 0.012 0.001 HIS F 463 PHE 0.023 0.002 PHE A 595 TYR 0.023 0.002 TYR B 607 ARG 0.003 0.000 ARG C 580 Details of bonding type rmsd hydrogen bonds : bond 0.03708 ( 1344) hydrogen bonds : angle 4.92512 ( 3834) covalent geometry : bond 0.00432 (31320) covalent geometry : angle 0.60704 (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 352 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 267 time to evaluate : 3.151 Fit side-chains REVERT: A 93 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7624 (tpt-90) REVERT: A 193 MET cc_start: 0.8053 (mtt) cc_final: 0.7797 (mtt) REVERT: A 239 MET cc_start: 0.8280 (tpp) cc_final: 0.8065 (tpp) REVERT: A 256 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: A 397 PHE cc_start: 0.7922 (t80) cc_final: 0.7650 (t80) REVERT: B 93 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7671 (tpt-90) REVERT: B 463 HIS cc_start: 0.6523 (t-170) cc_final: 0.6188 (t-170) REVERT: B 607 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.9144 (p90) REVERT: B 610 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6910 (tp30) REVERT: C 76 LEU cc_start: 0.8321 (tp) cc_final: 0.8055 (tt) REVERT: C 93 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7501 (tpt-90) REVERT: C 96 SER cc_start: 0.8710 (m) cc_final: 0.8164 (p) REVERT: C 256 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: C 324 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8258 (t) REVERT: C 434 ILE cc_start: 0.7727 (mt) cc_final: 0.7256 (mt) REVERT: C 444 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8489 (ptp90) REVERT: C 567 MET cc_start: 0.7516 (mmm) cc_final: 0.7297 (mmt) REVERT: D 93 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7624 (tpt-90) REVERT: D 193 MET cc_start: 0.8077 (mtt) cc_final: 0.7814 (mtt) REVERT: D 239 MET cc_start: 0.8246 (tpp) cc_final: 0.8033 (tpp) REVERT: D 256 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6432 (mp0) REVERT: D 397 PHE cc_start: 0.7916 (t80) cc_final: 0.7648 (t80) REVERT: E 76 LEU cc_start: 0.8311 (tp) cc_final: 0.8051 (tt) REVERT: E 93 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7495 (tpt-90) REVERT: E 96 SER cc_start: 0.8728 (m) cc_final: 0.8166 (p) REVERT: E 256 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: E 324 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.8245 (t) REVERT: E 434 ILE cc_start: 0.7731 (mt) cc_final: 0.7261 (mt) REVERT: E 444 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8478 (ptp90) REVERT: E 567 MET cc_start: 0.7508 (mmm) cc_final: 0.7278 (mmt) REVERT: E 610 GLU cc_start: 0.7216 (mm-30) cc_final: 0.7009 (tp30) REVERT: F 93 ARG cc_start: 0.8132 (mmm160) cc_final: 0.7672 (tpt-90) REVERT: F 463 HIS cc_start: 0.6502 (t-170) cc_final: 0.6163 (t-170) REVERT: F 607 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.9147 (p90) REVERT: F 610 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6933 (tp30) outliers start: 85 outliers final: 67 residues processed: 322 average time/residue: 0.3979 time to fit residues: 211.4119 Evaluate side-chains 336 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 259 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 227 VAL 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 607 TYR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 616 GLU 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 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 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 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 428 VAL 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 115 SER Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 403 LEU 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 615 ILE Chi-restraints excluded: chain F residue 616 GLU 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: 7.9990 chunk 20 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 373 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 372 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 ASN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 583 HIS E 158 ASN E 583 HIS F 158 ASN ** F 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 583 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.090283 restraints weight = 119643.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092943 restraints weight = 93816.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093329 restraints weight = 76166.272| |-----------------------------------------------------------------------------| 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 = 0.36 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 = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 31320 Z= 0.256 Angle : 0.674 12.495 42516 Z= 0.346 Chirality : 0.046 0.234 4842 Planarity : 0.005 0.046 5580 Dihedral : 4.869 47.351 4354 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.67 % Allowed : 15.79 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.13), residues: 4062 helix: 0.71 (0.13), residues: 1458 sheet: 0.32 (0.20), residues: 762 loop : -0.49 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 172 HIS 0.009 0.001 HIS F 463 PHE 0.024 0.002 PHE D 595 TYR 0.024 0.002 TYR B 607 ARG 0.004 0.001 ARG B 241 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 1344) hydrogen bonds : angle 5.12350 ( 3834) covalent geometry : bond 0.00609 (31320) covalent geometry : angle 0.67362 (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 345 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 260 time to evaluate : 3.445 Fit side-chains REVERT: A 93 ARG cc_start: 0.8178 (mmm160) cc_final: 0.7572 (tpt-90) REVERT: A 239 MET cc_start: 0.8375 (tpp) cc_final: 0.8156 (tpp) REVERT: A 256 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: A 397 PHE cc_start: 0.7988 (t80) cc_final: 0.7748 (t80) REVERT: B 93 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7615 (tpt170) REVERT: B 607 TYR cc_start: 0.9418 (OUTLIER) cc_final: 0.9211 (p90) REVERT: B 610 GLU cc_start: 0.7430 (mm-30) cc_final: 0.6988 (tp30) REVERT: C 76 LEU cc_start: 0.8333 (tp) cc_final: 0.8071 (tt) REVERT: C 93 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7627 (tpt-90) REVERT: C 211 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8781 (tt) REVERT: C 256 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6210 (mp0) REVERT: C 324 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8340 (t) REVERT: C 434 ILE cc_start: 0.7740 (mt) cc_final: 0.7281 (mt) REVERT: C 444 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8446 (ptp90) REVERT: C 567 MET cc_start: 0.7498 (mmm) cc_final: 0.7281 (mmt) REVERT: D 93 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7597 (tpt-90) REVERT: D 239 MET cc_start: 0.8356 (tpp) cc_final: 0.8138 (tpp) REVERT: D 256 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: D 397 PHE cc_start: 0.7986 (t80) cc_final: 0.7750 (t80) REVERT: E 76 LEU cc_start: 0.8326 (tp) cc_final: 0.8064 (tt) REVERT: E 93 ARG cc_start: 0.8257 (mmm160) cc_final: 0.7631 (tpt-90) REVERT: E 211 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8791 (tt) REVERT: E 256 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: E 324 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8352 (t) REVERT: E 434 ILE cc_start: 0.7751 (mt) cc_final: 0.7295 (mt) REVERT: E 444 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8432 (ptp90) REVERT: E 567 MET cc_start: 0.7498 (mmm) cc_final: 0.7278 (mmt) REVERT: E 610 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6928 (tp30) REVERT: F 93 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7616 (tpt170) REVERT: F 610 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6967 (tp30) outliers start: 85 outliers final: 64 residues processed: 314 average time/residue: 0.4007 time to fit residues: 208.1486 Evaluate side-chains 324 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 249 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 227 VAL 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 607 TYR Chi-restraints excluded: chain B residue 615 ILE Chi-restraints excluded: chain B residue 616 GLU 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 211 ILE 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 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 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 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 211 ILE 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 404 MET Chi-restraints excluded: chain E residue 428 VAL 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 115 SER Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 403 LEU 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 615 ILE Chi-restraints excluded: chain F residue 616 GLU 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: 1.9990 chunk 320 optimal weight: 0.0870 chunk 251 optimal weight: 6.9990 chunk 204 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 347 optimal weight: 3.9990 chunk 400 optimal weight: 0.1980 chunk 234 optimal weight: 0.1980 chunk 161 optimal weight: 5.9990 chunk 266 optimal weight: 0.9990 chunk 354 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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** ** B 408 ASN ** 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 = 0.3627 r_free = 0.3627 target = 0.116158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094581 restraints weight = 124478.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097353 restraints weight = 90464.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097707 restraints weight = 73742.361| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31320 Z= 0.108 Angle : 0.569 11.367 42516 Z= 0.291 Chirality : 0.043 0.176 4842 Planarity : 0.004 0.033 5580 Dihedral : 4.481 45.364 4352 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.76 % Allowed : 16.76 % Favored : 81.48 % 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: 0.88 (0.14), residues: 1494 sheet: 0.49 (0.20), residues: 786 loop : -0.36 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 651 HIS 0.012 0.001 HIS F 463 PHE 0.027 0.001 PHE B 595 TYR 0.019 0.001 TYR F 607 ARG 0.003 0.000 ARG C 281 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 1344) hydrogen bonds : angle 4.77615 ( 3834) covalent geometry : bond 0.00245 (31320) covalent geometry : angle 0.56878 (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 340 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 3.120 Fit side-chains REVERT: A 93 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7638 (tpt-90) REVERT: A 193 MET cc_start: 0.8024 (mtt) cc_final: 0.7618 (mtt) REVERT: A 256 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: A 397 PHE cc_start: 0.7828 (t80) cc_final: 0.7591 (t80) REVERT: A 567 MET cc_start: 0.7655 (mmm) cc_final: 0.7306 (mmt) REVERT: A 622 ASP cc_start: 0.7656 (m-30) cc_final: 0.7244 (m-30) REVERT: B 93 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7426 (tpp-160) REVERT: B 610 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6768 (tp30) REVERT: C 76 LEU cc_start: 0.8324 (tp) cc_final: 0.8039 (tt) REVERT: C 93 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7478 (tpt-90) REVERT: C 96 SER cc_start: 0.8702 (m) cc_final: 0.8136 (p) REVERT: C 256 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: C 324 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8262 (t) REVERT: C 444 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8441 (ptp90) REVERT: C 567 MET cc_start: 0.7464 (mmm) cc_final: 0.7225 (mmt) REVERT: D 93 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7639 (tpt-90) REVERT: D 193 MET cc_start: 0.8033 (mtt) cc_final: 0.7664 (mtt) REVERT: D 256 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: D 397 PHE cc_start: 0.7830 (t80) cc_final: 0.7608 (t80) REVERT: D 567 MET cc_start: 0.7617 (mmm) cc_final: 0.7255 (mmt) REVERT: D 622 ASP cc_start: 0.7688 (m-30) cc_final: 0.7315 (m-30) REVERT: E 76 LEU cc_start: 0.8322 (tp) cc_final: 0.8030 (tt) REVERT: E 93 ARG cc_start: 0.8164 (mmm160) cc_final: 0.7491 (tpt-90) REVERT: E 96 SER cc_start: 0.8716 (m) cc_final: 0.8179 (p) REVERT: E 256 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: E 324 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8266 (t) REVERT: E 444 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8428 (ptp90) REVERT: E 567 MET cc_start: 0.7434 (mmm) cc_final: 0.7206 (mmt) REVERT: F 93 ARG cc_start: 0.8095 (mmm160) cc_final: 0.7420 (tpp-160) REVERT: F 610 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6755 (tp30) outliers start: 56 outliers final: 43 residues processed: 322 average time/residue: 0.4065 time to fit residues: 214.5492 Evaluate side-chains 308 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 257 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER 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 522 ASP Chi-restraints excluded: chain A residue 538 ASP 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 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 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 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 663 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 522 ASP Chi-restraints excluded: chain D residue 538 ASP Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain D residue 670 THR 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 404 MET Chi-restraints excluded: chain E residue 428 VAL 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 670 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 403 LEU 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: 8.9990 chunk 281 optimal weight: 0.0010 chunk 189 optimal weight: 0.6980 chunk 345 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 331 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 340 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.7392 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.114795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093072 restraints weight = 123796.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095739 restraints weight = 92818.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096131 restraints weight = 76864.202| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 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 = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31320 Z= 0.148 Angle : 0.591 11.913 42516 Z= 0.301 Chirality : 0.043 0.196 4842 Planarity : 0.004 0.033 5580 Dihedral : 4.404 17.989 4350 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.67 % Allowed : 17.14 % Favored : 81.19 % 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: 0.40 (0.13), residues: 4062 helix: 0.90 (0.13), residues: 1530 sheet: 0.68 (0.20), residues: 756 loop : -0.39 (0.14), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 651 HIS 0.010 0.001 HIS B 463 PHE 0.024 0.002 PHE D 595 TYR 0.021 0.002 TYR F 607 ARG 0.003 0.000 ARG C 281 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 1344) hydrogen bonds : angle 4.82270 ( 3834) covalent geometry : bond 0.00352 (31320) covalent geometry : angle 0.59095 (42516) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9347.12 seconds wall clock time: 164 minutes 53.19 seconds (9893.19 seconds total)