Starting phenix.real_space_refine on Fri Mar 6 11:29:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jql_9873/03_2026/6jql_9873.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jql_9873/03_2026/6jql_9873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jql_9873/03_2026/6jql_9873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jql_9873/03_2026/6jql_9873.map" model { file = "/net/cci-nas-00/data/ceres_data/6jql_9873/03_2026/6jql_9873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jql_9873/03_2026/6jql_9873.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 19344 2.51 5 N 5424 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 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30648 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "C" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "D" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "E" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Chain: "F" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5108 Classifications: {'peptide': 678} Link IDs: {'PTRANS': 35, 'TRANS': 642} Time building chain proxies: 6.69, per 1000 atoms: 0.22 Number of scatterers: 30648 At special positions: 0 Unit cell: (178.08, 174.9, 109.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 5730 8.00 N 5424 7.00 C 19344 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: 2.51 Conformation dependent library (CDL) restraints added in 1.4 seconds 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7404 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 44 sheets defined 39.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.683A pdb=" N MET A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.742A pdb=" N GLU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 92 through 117 removed outlier: 3.796A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 175 removed outlier: 4.123A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 169 " --> pdb=" O LEU A 165 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.048A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.714A pdb=" N LEU A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 273 through 289 removed outlier: 4.306A 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 320 removed outlier: 4.294A pdb=" N VAL A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 354 Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.683A pdb=" N GLN A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.691A pdb=" N ASP A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 485 through 492 removed outlier: 3.851A pdb=" N ALA A 489 " --> pdb=" O GLY A 486 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 490 " --> pdb=" O LEU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 511 removed outlier: 3.953A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) 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: 3.643A pdb=" N ALA A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 573 " --> pdb=" O LYS A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 Processing helix chain 'B' and resid 40 through 58 removed outlier: 4.067A pdb=" N ALA B 53 " --> pdb=" O ILE B 49 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.719A pdb=" N GLU B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 92 through 117 removed outlier: 3.722A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 174 removed outlier: 4.236A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 186 through 199 removed outlier: 4.134A pdb=" N THR B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 4.002A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.591A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.299A 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 320 removed outlier: 4.129A pdb=" N VAL B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.662A pdb=" N LYS B 349 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.663A pdb=" N GLN B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.641A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 485 through 489 removed outlier: 3.699A pdb=" N ALA B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.052A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) 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: 3.524A pdb=" N ALA B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 573 " --> pdb=" O LYS B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 596 Processing helix chain 'C' and resid 40 through 52 Processing helix chain 'C' and resid 52 through 59 removed outlier: 3.633A pdb=" N MET C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.782A pdb=" N GLU C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 92 through 117 removed outlier: 3.686A pdb=" N VAL C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 174 removed outlier: 4.103A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Proline residue: C 170 - end of helix Processing helix chain 'C' and resid 186 through 199 removed outlier: 4.054A pdb=" N THR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.665A pdb=" N LEU C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.652A pdb=" N MET C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 Processing helix chain 'C' and resid 273 through 289 removed outlier: 4.254A 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 320 removed outlier: 4.219A pdb=" N VAL C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 354 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.817A pdb=" N GLN C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.662A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 443 " --> pdb=" O ILE C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 485 through 492 removed outlier: 3.753A pdb=" N ALA C 489 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL C 490 " --> pdb=" O LEU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 510 removed outlier: 3.855A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) 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: 3.500A pdb=" N ALA C 573 " --> pdb=" O LYS C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 596 Processing helix chain 'D' and resid 40 through 58 removed outlier: 4.050A pdb=" N ALA D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) Proline residue: D 54 - end of helix Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.720A pdb=" N GLU D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 92 through 117 removed outlier: 4.155A pdb=" N GLY D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 175 removed outlier: 4.233A pdb=" N LYS D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA D 169 " --> pdb=" O LEU D 165 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 186 through 199 removed outlier: 4.068A pdb=" N THR D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.917A pdb=" N LEU D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 242 removed outlier: 3.558A pdb=" N GLY D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 Processing helix chain 'D' and resid 273 through 289 removed outlier: 4.400A 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 320 removed outlier: 3.941A pdb=" N VAL D 316 " --> pdb=" O SER D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 355 removed outlier: 3.704A pdb=" N LYS D 349 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 3.555A pdb=" N GLU D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 384 through 388' Processing helix chain 'D' and resid 410 through 418 removed outlier: 3.658A pdb=" N GLN D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.672A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 502 through 511 removed outlier: 4.029A pdb=" N ALA D 508 " --> pdb=" O THR D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 529 Processing helix chain 'D' and resid 530 through 534 Processing helix chain 'D' and resid 548 through 560 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 569 through 574 Processing helix chain 'D' and resid 583 through 596 Processing helix chain 'E' and resid 40 through 52 Processing helix chain 'E' and resid 52 through 59 removed outlier: 3.709A pdb=" N MET E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.739A pdb=" N GLU E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 92 through 117 removed outlier: 3.928A pdb=" N VAL E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 99 " --> pdb=" O ASP E 95 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 174 removed outlier: 4.062A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 186 through 199 removed outlier: 4.094A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.695A pdb=" N LEU E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.599A pdb=" N MET E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 250 Processing helix chain 'E' and resid 273 through 289 removed outlier: 4.282A 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 320 removed outlier: 4.221A pdb=" N VAL E 316 " --> pdb=" O SER E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 354 Processing helix chain 'E' and resid 410 through 418 removed outlier: 3.855A pdb=" N GLN E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.673A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 443 " --> pdb=" O ILE E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 485 through 492 removed outlier: 3.791A pdb=" N ALA E 489 " --> pdb=" O GLY E 486 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL E 490 " --> pdb=" O LEU E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 511 removed outlier: 3.920A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) 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: 3.501A pdb=" N ALA E 572 " --> pdb=" O ASP E 568 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 removed outlier: 3.519A pdb=" N VAL E 596 " --> pdb=" O ALA E 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 58 removed outlier: 3.969A pdb=" N ALA F 53 " --> pdb=" O ILE F 49 " (cutoff:3.500A) Proline residue: F 54 - end of helix Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.732A pdb=" N GLU F 78 " --> pdb=" O HIS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'F' and resid 92 through 117 removed outlier: 4.109A pdb=" N GLY F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 166 Processing helix chain 'F' and resid 168 through 175 Processing helix chain 'F' and resid 186 through 199 removed outlier: 4.085A pdb=" N THR F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 removed outlier: 4.043A pdb=" N LEU F 222 " --> pdb=" O LEU F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 242 removed outlier: 3.514A pdb=" N GLY F 237 " --> pdb=" O SER F 233 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL F 242 " --> pdb=" O GLN F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 250 Processing helix chain 'F' and resid 273 through 289 removed outlier: 4.407A 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 320 removed outlier: 4.033A pdb=" N VAL F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 355 removed outlier: 3.673A pdb=" N LYS F 349 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 388 removed outlier: 3.545A pdb=" N GLU F 387 " --> pdb=" O GLN F 384 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 384 through 388' Processing helix chain 'F' and resid 410 through 418 removed outlier: 3.600A pdb=" N GLN F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.702A pdb=" N ASP F 441 " --> pdb=" O GLN F 437 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 502 through 511 removed outlier: 4.094A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 534 Processing helix chain 'F' and resid 548 through 560 Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 569 through 574 Processing helix chain 'F' and resid 583 through 596 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 23 Processing sheet with id=AA3, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.661A pdb=" N GLY B 425 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 452 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 427 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASN B 261 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.127A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.924A pdb=" N TYR A 381 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 380 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 261 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 425 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 452 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 427 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 449 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 358 through 359 removed outlier: 3.924A pdb=" N TYR A 381 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU A 380 " --> pdb=" O LEU A 403 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN A 261 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY A 425 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU A 452 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 427 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 449 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 539 through 541 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.415A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 671 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AB1, first strand: chain 'A' and resid 612 through 613 Processing sheet with id=AB2, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AB3, first strand: chain 'B' and resid 20 through 23 removed outlier: 3.595A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 208 through 210 removed outlier: 6.003A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL B 152 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 539 through 541 Processing sheet with id=AB6, first strand: chain 'B' and resid 539 through 541 removed outlier: 5.212A pdb=" N VAL B 626 " --> pdb=" O PHE B 656 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE B 656 " --> pdb=" O VAL B 626 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 628 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLU B 654 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N CYS B 630 " --> pdb=" O ALA B 652 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA B 652 " --> pdb=" O CYS B 630 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 655 " --> pdb=" O ALA B 664 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ALA B 664 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 671 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AB9, first strand: chain 'C' and resid 130 through 131 removed outlier: 6.580A pdb=" N GLY D 425 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU D 452 " --> pdb=" O GLY D 425 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU D 427 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN D 261 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG D 299 " --> pdb=" O THR D 402 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N MET D 404 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE D 301 " --> pdb=" O MET D 404 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ALA D 406 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL D 303 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N THR D 378 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU D 403 " --> pdb=" O THR D 378 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.192A pdb=" N ALA C 151 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LYS C 181 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N HIS C 153 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.843A pdb=" N TYR C 381 " --> pdb=" O CYS C 358 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG C 299 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 261 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 449 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.843A pdb=" N TYR C 381 " --> pdb=" O CYS C 358 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ARG C 299 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN C 261 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE C 449 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 520 through 521 removed outlier: 6.268A pdb=" N GLU C 520 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 541 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 538 " --> pdb=" O CYS C 630 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 520 through 521 removed outlier: 6.268A pdb=" N GLU C 520 " --> pdb=" O SER C 539 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU C 541 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C 538 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL C 626 " --> pdb=" O PHE C 656 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE C 656 " --> pdb=" O VAL C 626 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LEU C 628 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU C 654 " --> pdb=" O LEU C 628 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N CYS C 630 " --> pdb=" O ALA C 652 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ALA C 652 " --> pdb=" O CYS C 630 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU C 671 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AC7, first strand: chain 'C' and resid 612 through 613 removed outlier: 6.202A pdb=" N VAL D 603 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 673 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 669 " --> pdb=" O TYR D 607 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D 609 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER D 667 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 629 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 612 through 613 removed outlier: 6.202A pdb=" N VAL D 603 " --> pdb=" O ALA D 673 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA D 673 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 669 " --> pdb=" O TYR D 607 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D 609 " --> pdb=" O SER D 667 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N SER D 667 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU D 650 " --> pdb=" O LYS D 631 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 629 " --> pdb=" O ALA D 652 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AD1, first strand: chain 'D' and resid 20 through 23 removed outlier: 3.610A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.107A pdb=" N ALA D 151 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LYS D 181 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N HIS D 153 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AD4, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.509A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 removed outlier: 6.613A pdb=" N GLY F 425 " --> pdb=" O GLN F 450 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU F 452 " --> pdb=" O GLY F 425 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU F 427 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ASN F 261 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG F 299 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N MET F 404 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE F 301 " --> pdb=" O MET F 404 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA F 406 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL F 303 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR F 378 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU F 403 " --> pdb=" O THR F 378 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 208 through 210 removed outlier: 6.689A pdb=" N ALA E 178 " --> pdb=" O SER E 209 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA E 151 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N LYS E 181 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS E 153 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.997A pdb=" N TYR E 381 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG E 299 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 449 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.997A pdb=" N TYR E 381 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ARG E 299 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 449 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 539 through 541 Processing sheet with id=AE1, first strand: chain 'E' and resid 539 through 541 removed outlier: 5.069A pdb=" N VAL E 626 " --> pdb=" O PHE E 656 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE E 656 " --> pdb=" O VAL E 626 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU E 628 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU E 654 " --> pdb=" O LEU E 628 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N CYS E 630 " --> pdb=" O ALA E 652 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA E 652 " --> pdb=" O CYS E 630 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU E 671 " --> pdb=" O ILE E 604 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 608 through 609 Processing sheet with id=AE3, first strand: chain 'E' and resid 612 through 613 Processing sheet with id=AE4, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AE5, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.544A pdb=" N TRP F 32 " --> pdb=" O ILE F 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 208 through 210 removed outlier: 5.959A pdb=" N ALA F 151 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS F 181 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N HIS F 153 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 152 " --> pdb=" O THR F 229 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 539 through 541 Processing sheet with id=AE8, first strand: chain 'F' and resid 539 through 541 removed outlier: 3.664A pdb=" N THR F 629 " --> pdb=" O ALA F 652 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU F 650 " --> pdb=" O LYS F 631 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 671 " --> pdb=" O ILE F 604 " (cutoff:3.500A) 1366 hydrogen bonds defined for protein. 3777 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.90 Time building geometry restraints manager: 3.29 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: 9933 1.34 - 1.46: 4689 1.46 - 1.58: 16404 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 31266 Sorted by residual: bond pdb=" C TRP D 124 " pdb=" O TRP D 124 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.17e+00 bond pdb=" N THR A 634 " pdb=" CA THR A 634 " ideal model delta sigma weight residual 1.461 1.481 -0.020 1.38e-02 5.25e+03 2.08e+00 bond pdb=" C ALA C 53 " pdb=" N PRO C 54 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 2.03e+00 bond pdb=" C ALA B 53 " pdb=" N PRO B 54 " ideal model delta sigma weight residual 1.336 1.354 -0.018 1.25e-02 6.40e+03 1.99e+00 bond pdb=" N THR D 634 " pdb=" CA THR D 634 " ideal model delta sigma weight residual 1.461 1.480 -0.019 1.38e-02 5.25e+03 1.98e+00 ... (remaining 31261 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 40989 1.92 - 3.84: 1226 3.84 - 5.76: 154 5.76 - 7.68: 50 7.68 - 9.60: 19 Bond angle restraints: 42438 Sorted by residual: angle pdb=" C VAL B 514 " pdb=" N ARG B 515 " pdb=" CA ARG B 515 " ideal model delta sigma weight residual 120.38 126.44 -6.06 1.37e+00 5.33e-01 1.96e+01 angle pdb=" N GLY E 608 " pdb=" CA GLY E 608 " pdb=" C GLY E 608 " ideal model delta sigma weight residual 110.87 116.93 -6.06 1.54e+00 4.22e-01 1.55e+01 angle pdb=" C ASN B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta sigma weight residual 121.54 128.29 -6.75 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ASN C 606 " pdb=" N TYR C 607 " pdb=" CA TYR C 607 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ASN E 606 " pdb=" N TYR E 607 " pdb=" CA TYR E 607 " ideal model delta sigma weight residual 121.54 128.28 -6.74 1.91e+00 2.74e-01 1.25e+01 ... (remaining 42433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 17826 15.45 - 30.90: 678 30.90 - 46.35: 258 46.35 - 61.81: 6 61.81 - 77.26: 18 Dihedral angle restraints: 18786 sinusoidal: 7266 harmonic: 11520 Sorted by residual: dihedral pdb=" CA GLU C 521 " pdb=" C GLU C 521 " pdb=" N ASP C 522 " pdb=" CA ASP C 522 " ideal model delta harmonic sigma weight residual -180.00 -156.02 -23.98 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP D 522 " pdb=" C ASP D 522 " pdb=" N ARG D 523 " pdb=" CA ARG D 523 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ASP F 522 " pdb=" C ASP F 522 " pdb=" N ARG F 523 " pdb=" CA ARG F 523 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 18783 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2980 0.040 - 0.079: 1257 0.079 - 0.119: 491 0.119 - 0.158: 95 0.158 - 0.198: 13 Chirality restraints: 4836 Sorted by residual: chirality pdb=" CA TYR F 607 " pdb=" N TYR F 607 " pdb=" C TYR F 607 " pdb=" CB TYR F 607 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA TYR E 607 " pdb=" N TYR E 607 " pdb=" C TYR E 607 " pdb=" CB TYR E 607 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CB VAL F 514 " pdb=" CA VAL F 514 " pdb=" CG1 VAL F 514 " pdb=" CG2 VAL F 514 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.46e-01 ... (remaining 4833 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 398 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO A 399 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 399 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 399 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 124 " -0.013 2.00e-02 2.50e+03 1.46e-02 5.30e+00 pdb=" CG TRP C 124 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 124 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 124 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 124 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 124 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 124 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 124 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 124 " -0.012 2.00e-02 2.50e+03 1.45e-02 5.23e+00 pdb=" CG TRP E 124 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP E 124 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP E 124 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 124 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 124 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 124 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 124 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 124 " -0.002 2.00e-02 2.50e+03 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.82: 9171 2.82 - 3.34: 27230 3.34 - 3.86: 53926 3.86 - 4.38: 61769 4.38 - 4.90: 108583 Nonbonded interactions: 260679 Sorted by model distance: nonbonded pdb=" OG SER F 19 " pdb=" OE1 GLU F 33 " model vdw 2.305 3.040 nonbonded pdb=" OG SER E 36 " pdb=" O SER E 214 " model vdw 2.310 3.040 nonbonded pdb=" OG SER A 36 " pdb=" O SER A 214 " model vdw 2.318 3.040 nonbonded pdb=" OD2 ASP C 127 " pdb=" ND1 HIS C 142 " model vdw 2.326 3.120 nonbonded pdb=" OD2 ASP B 127 " pdb=" ND1 HIS B 142 " model vdw 2.327 3.120 ... (remaining 260674 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.700 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.020 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31266 Z= 0.190 Angle : 0.811 9.596 42438 Z= 0.435 Chirality : 0.050 0.198 4836 Planarity : 0.007 0.058 5568 Dihedral : 10.099 77.256 11382 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.01 (0.10), residues: 4056 helix: -2.80 (0.10), residues: 1338 sheet: -2.65 (0.16), residues: 720 loop : -2.49 (0.11), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 361 TYR 0.014 0.002 TYR A 607 PHE 0.023 0.003 PHE A 595 TRP 0.038 0.003 TRP C 124 HIS 0.010 0.002 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00411 (31266) covalent geometry : angle 0.81102 (42438) hydrogen bonds : bond 0.18404 ( 1267) hydrogen bonds : angle 8.79798 ( 3777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 796 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8739 (tp) cc_final: 0.8469 (mm) REVERT: A 411 HIS cc_start: 0.7745 (t-170) cc_final: 0.7229 (t-170) REVERT: B 26 ILE cc_start: 0.7952 (tp) cc_final: 0.7737 (mm) REVERT: B 120 ASP cc_start: 0.7634 (t0) cc_final: 0.7129 (t0) REVERT: B 199 ASP cc_start: 0.7120 (m-30) cc_final: 0.6884 (p0) REVERT: B 309 ASN cc_start: 0.7718 (m110) cc_final: 0.7230 (m110) REVERT: B 423 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8774 (tp) REVERT: B 437 GLN cc_start: 0.7719 (mt0) cc_final: 0.7404 (mp10) REVERT: C 26 ILE cc_start: 0.8768 (tp) cc_final: 0.8488 (mm) REVERT: C 386 ASP cc_start: 0.7255 (p0) cc_final: 0.6432 (p0) REVERT: D 120 ASP cc_start: 0.7584 (t0) cc_final: 0.7122 (t0) REVERT: D 199 ASP cc_start: 0.7352 (m-30) cc_final: 0.7024 (p0) REVERT: D 504 THR cc_start: 0.9137 (t) cc_final: 0.8798 (m) REVERT: E 26 ILE cc_start: 0.8739 (tp) cc_final: 0.8386 (mm) REVERT: E 122 THR cc_start: 0.8424 (m) cc_final: 0.8141 (p) REVERT: E 196 SER cc_start: 0.8555 (m) cc_final: 0.8242 (t) REVERT: E 220 ASP cc_start: 0.7827 (m-30) cc_final: 0.7571 (m-30) REVERT: E 351 ASN cc_start: 0.8489 (m-40) cc_final: 0.8080 (m-40) REVERT: E 411 HIS cc_start: 0.7764 (t-170) cc_final: 0.7454 (t-170) REVERT: E 459 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6599 (pt0) REVERT: F 120 ASP cc_start: 0.7571 (t0) cc_final: 0.7131 (t0) REVERT: F 504 THR cc_start: 0.8805 (t) cc_final: 0.8516 (m) outliers start: 5 outliers final: 3 residues processed: 801 average time/residue: 0.8456 time to fit residues: 769.4430 Evaluate side-chains 358 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 354 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain F residue 648 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 GLN A 500 GLN A 660 GLN ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 153 HIS B 261 ASN B 411 HIS B 500 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 GLN C 500 GLN ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 554 ASN D 24 HIS D 46 GLN D 74 HIS D 153 HIS D 158 ASN D 191 GLN D 305 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 GLN ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 153 HIS E 320 GLN E 329 GLN E 347 GLN E 500 GLN ** E 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 554 ASN E 660 GLN F 24 HIS ** F 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 GLN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091194 restraints weight = 44321.581| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.79 r_work: 0.2914 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 31266 Z= 0.249 Angle : 0.685 10.565 42438 Z= 0.353 Chirality : 0.047 0.193 4836 Planarity : 0.006 0.049 5568 Dihedral : 5.109 34.573 4338 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.00 % Allowed : 11.88 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4056 helix: -0.95 (0.12), residues: 1422 sheet: -1.96 (0.17), residues: 762 loop : -1.90 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 361 TYR 0.017 0.002 TYR F 607 PHE 0.034 0.002 PHE E 595 TRP 0.031 0.002 TRP F 124 HIS 0.017 0.002 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00578 (31266) covalent geometry : angle 0.68508 (42438) hydrogen bonds : bond 0.04016 ( 1267) hydrogen bonds : angle 5.58676 ( 3777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 363 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7003 (ppt170) cc_final: 0.6790 (pmt-80) REVERT: A 26 ILE cc_start: 0.8839 (tp) cc_final: 0.8566 (mm) REVERT: A 51 LYS cc_start: 0.8785 (mmtp) cc_final: 0.8482 (mmtm) REVERT: A 83 TYR cc_start: 0.8686 (m-80) cc_final: 0.8469 (m-80) REVERT: A 205 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6447 (pp20) REVERT: A 524 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8288 (pt) REVERT: B 26 ILE cc_start: 0.8192 (tp) cc_final: 0.7935 (mm) REVERT: B 120 ASP cc_start: 0.8360 (t0) cc_final: 0.7921 (t0) REVERT: B 293 GLN cc_start: 0.8396 (mt0) cc_final: 0.7617 (mt0) REVERT: B 334 MET cc_start: 0.8559 (ttm) cc_final: 0.8267 (ttm) REVERT: B 423 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9012 (tp) REVERT: B 437 GLN cc_start: 0.8262 (mt0) cc_final: 0.7852 (mp10) REVERT: C 26 ILE cc_start: 0.8868 (tp) cc_final: 0.8616 (mm) REVERT: C 122 THR cc_start: 0.8792 (m) cc_final: 0.8588 (p) REVERT: C 567 MET cc_start: 0.9253 (mmp) cc_final: 0.8969 (mmm) REVERT: D 120 ASP cc_start: 0.8353 (t0) cc_final: 0.7963 (t0) REVERT: D 345 ASP cc_start: 0.7373 (m-30) cc_final: 0.7127 (m-30) REVERT: D 429 THR cc_start: 0.9418 (p) cc_final: 0.9192 (t) REVERT: D 433 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8117 (mm-40) REVERT: D 504 THR cc_start: 0.9403 (t) cc_final: 0.8988 (m) REVERT: E 26 ILE cc_start: 0.8785 (tp) cc_final: 0.8508 (mm) REVERT: E 122 THR cc_start: 0.8970 (m) cc_final: 0.8707 (p) REVERT: E 161 CYS cc_start: 0.8958 (m) cc_final: 0.8687 (t) REVERT: E 205 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6521 (pp20) REVERT: E 220 ASP cc_start: 0.8904 (m-30) cc_final: 0.8549 (m-30) REVERT: E 629 THR cc_start: 0.9190 (t) cc_final: 0.8963 (m) REVERT: F 20 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.7299 (mtp-110) REVERT: F 120 ASP cc_start: 0.8443 (t0) cc_final: 0.7973 (t0) REVERT: F 293 GLN cc_start: 0.8293 (mt0) cc_final: 0.7885 (mt0) REVERT: F 414 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: F 437 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: F 469 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8462 (pt0) REVERT: F 504 THR cc_start: 0.9217 (t) cc_final: 0.8825 (m) REVERT: F 616 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: F 632 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8507 (ttt180) outliers start: 127 outliers final: 36 residues processed: 458 average time/residue: 0.7709 time to fit residues: 405.0229 Evaluate side-chains 330 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 437 GLN Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 190 optimal weight: 4.9990 chunk 238 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 225 optimal weight: 0.6980 chunk 278 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 366 optimal weight: 0.0770 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN D 347 GLN D 411 HIS ** D 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN F 347 GLN ** F 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.089401 restraints weight = 45080.809| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.90 r_work: 0.2884 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 31266 Z= 0.204 Angle : 0.623 8.710 42438 Z= 0.318 Chirality : 0.045 0.157 4836 Planarity : 0.005 0.044 5568 Dihedral : 4.879 33.911 4336 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.65 % Allowed : 13.45 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.13), residues: 4056 helix: -0.29 (0.13), residues: 1464 sheet: -1.78 (0.17), residues: 786 loop : -1.62 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 361 TYR 0.024 0.002 TYR A 607 PHE 0.027 0.002 PHE F 595 TRP 0.017 0.002 TRP C 124 HIS 0.016 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00471 (31266) covalent geometry : angle 0.62344 (42438) hydrogen bonds : bond 0.03672 ( 1267) hydrogen bonds : angle 5.22766 ( 3777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 312 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7419 (pp20) cc_final: 0.7207 (pp20) REVERT: A 135 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: A 205 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6438 (pp20) REVERT: A 524 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8322 (pt) REVERT: A 567 MET cc_start: 0.9232 (mmp) cc_final: 0.9024 (mmm) REVERT: B 26 ILE cc_start: 0.8136 (tp) cc_final: 0.7881 (mm) REVERT: B 120 ASP cc_start: 0.8419 (t0) cc_final: 0.8044 (t0) REVERT: B 334 MET cc_start: 0.8555 (ttm) cc_final: 0.8207 (ttm) REVERT: B 437 GLN cc_start: 0.8339 (mt0) cc_final: 0.7847 (mp10) REVERT: B 469 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8932 (pt0) REVERT: B 549 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: C 26 ILE cc_start: 0.8774 (tp) cc_final: 0.8574 (mm) REVERT: C 33 GLU cc_start: 0.7394 (pp20) cc_final: 0.7190 (pp20) REVERT: C 78 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8487 (pt0) REVERT: C 122 THR cc_start: 0.8826 (m) cc_final: 0.8609 (p) REVERT: C 281 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8129 (ttt90) REVERT: C 351 ASN cc_start: 0.8657 (m-40) cc_final: 0.8406 (m-40) REVERT: C 361 ARG cc_start: 0.7407 (mtp-110) cc_final: 0.7165 (mtp85) REVERT: C 567 MET cc_start: 0.9207 (mmp) cc_final: 0.8913 (mmm) REVERT: D 120 ASP cc_start: 0.8460 (t0) cc_final: 0.8030 (t0) REVERT: D 134 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8325 (mttm) REVERT: D 287 MET cc_start: 0.8335 (ttm) cc_final: 0.8060 (mtp) REVERT: D 345 ASP cc_start: 0.7323 (m-30) cc_final: 0.7022 (m-30) REVERT: D 429 THR cc_start: 0.9455 (p) cc_final: 0.9203 (t) REVERT: D 433 GLN cc_start: 0.8329 (mm-40) cc_final: 0.7994 (mm-40) REVERT: D 610 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7736 (tp30) REVERT: D 616 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8465 (tt0) REVERT: E 21 LEU cc_start: 0.8439 (pt) cc_final: 0.8185 (pt) REVERT: E 26 ILE cc_start: 0.8703 (tp) cc_final: 0.8499 (mm) REVERT: E 33 GLU cc_start: 0.7520 (pp20) cc_final: 0.7283 (pp20) REVERT: E 78 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8343 (pp20) REVERT: E 122 THR cc_start: 0.8982 (m) cc_final: 0.8700 (p) REVERT: E 135 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: E 205 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6561 (pp20) REVERT: E 220 ASP cc_start: 0.8937 (m-30) cc_final: 0.8484 (m-30) REVERT: E 243 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7758 (tm-30) REVERT: E 606 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8183 (t0) REVERT: F 120 ASP cc_start: 0.8489 (t0) cc_final: 0.7989 (t0) REVERT: F 293 GLN cc_start: 0.8126 (mt0) cc_final: 0.7858 (mt0) REVERT: F 309 ASN cc_start: 0.8339 (m110) cc_final: 0.8113 (m-40) REVERT: F 414 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.7883 (mt0) REVERT: F 504 THR cc_start: 0.9199 (t) cc_final: 0.8808 (m) REVERT: F 616 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: F 632 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8497 (ttt180) REVERT: F 643 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7094 (mm-30) outliers start: 116 outliers final: 35 residues processed: 406 average time/residue: 0.7903 time to fit residues: 368.7083 Evaluate side-chains 338 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 287 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 78 GLU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 217 ASP Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 643 GLU Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 316 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 300 optimal weight: 7.9990 chunk 253 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 201 optimal weight: 7.9990 chunk 132 optimal weight: 0.4980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 HIS B 293 GLN B 433 GLN B 525 HIS C 46 GLN D 46 GLN D 158 ASN D 347 GLN D 411 HIS E 24 HIS ** F 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 433 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.114166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.088396 restraints weight = 44661.410| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.84 r_work: 0.2868 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 31266 Z= 0.216 Angle : 0.625 8.729 42438 Z= 0.317 Chirality : 0.045 0.179 4836 Planarity : 0.005 0.043 5568 Dihedral : 4.817 22.398 4334 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.69 % Allowed : 14.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 4056 helix: 0.01 (0.13), residues: 1476 sheet: -1.52 (0.18), residues: 774 loop : -1.52 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 141 TYR 0.018 0.002 TYR A 607 PHE 0.026 0.002 PHE E 595 TRP 0.014 0.001 TRP C 124 HIS 0.013 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00503 (31266) covalent geometry : angle 0.62498 (42438) hydrogen bonds : bond 0.03584 ( 1267) hydrogen bonds : angle 5.08368 ( 3777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 323 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7408 (pp20) cc_final: 0.7176 (pp20) REVERT: A 524 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8345 (pt) REVERT: A 567 MET cc_start: 0.9255 (mmp) cc_final: 0.8741 (mmp) REVERT: B 26 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7932 (mm) REVERT: B 120 ASP cc_start: 0.8454 (t0) cc_final: 0.8066 (t0) REVERT: B 334 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8145 (ttm) REVERT: B 414 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: B 437 GLN cc_start: 0.8419 (mt0) cc_final: 0.8027 (mp10) REVERT: B 549 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7681 (tt0) REVERT: B 567 MET cc_start: 0.8607 (mmm) cc_final: 0.8337 (mmm) REVERT: C 20 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7092 (ttm170) REVERT: C 26 ILE cc_start: 0.8779 (tp) cc_final: 0.8519 (mm) REVERT: C 33 GLU cc_start: 0.7423 (pp20) cc_final: 0.7169 (pp20) REVERT: C 351 ASN cc_start: 0.8780 (m-40) cc_final: 0.8531 (m-40) REVERT: C 551 ASP cc_start: 0.8681 (m-30) cc_final: 0.8433 (m-30) REVERT: C 567 MET cc_start: 0.9265 (mmp) cc_final: 0.8967 (mmm) REVERT: D 120 ASP cc_start: 0.8538 (t0) cc_final: 0.8170 (t0) REVERT: D 164 MET cc_start: 0.9074 (ttt) cc_final: 0.8735 (ttp) REVERT: D 287 MET cc_start: 0.8373 (ttm) cc_final: 0.8130 (mtp) REVERT: D 345 ASP cc_start: 0.7314 (m-30) cc_final: 0.7095 (m-30) REVERT: D 433 GLN cc_start: 0.8420 (mm-40) cc_final: 0.7995 (mm110) REVERT: D 610 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7728 (tp30) REVERT: E 21 LEU cc_start: 0.8414 (pt) cc_final: 0.8206 (pt) REVERT: E 33 GLU cc_start: 0.7549 (pp20) cc_final: 0.7269 (pp20) REVERT: E 78 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8357 (pp20) REVERT: E 122 THR cc_start: 0.8972 (m) cc_final: 0.8731 (p) REVERT: E 135 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: E 205 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6490 (pp20) REVERT: E 220 ASP cc_start: 0.8934 (m-30) cc_final: 0.8466 (m-30) REVERT: E 243 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: E 606 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8176 (t0) REVERT: F 78 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7607 (pp20) REVERT: F 120 ASP cc_start: 0.8559 (t0) cc_final: 0.8091 (t0) REVERT: F 293 GLN cc_start: 0.8300 (mt0) cc_final: 0.8020 (mt0) REVERT: F 361 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7219 (ttt-90) REVERT: F 414 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: F 504 THR cc_start: 0.9213 (t) cc_final: 0.8811 (m) REVERT: F 616 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: F 632 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8549 (ttt180) outliers start: 117 outliers final: 49 residues processed: 409 average time/residue: 0.7786 time to fit residues: 365.7201 Evaluate side-chains 347 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 GLU Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 505 MET Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 334 MET Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 632 ARG Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 414 GLN Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 255 MET Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 244 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 176 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 391 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 312 optimal weight: 0.8980 chunk 230 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 606 ASN ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN C 659 HIS D 347 GLN D 411 HIS ** E 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 659 HIS F 411 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.091672 restraints weight = 43318.148| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.84 r_work: 0.2907 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 31266 Z= 0.129 Angle : 0.555 7.654 42438 Z= 0.283 Chirality : 0.042 0.143 4836 Planarity : 0.004 0.041 5568 Dihedral : 4.516 20.070 4334 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.28 % Allowed : 15.25 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 4056 helix: 0.37 (0.14), residues: 1470 sheet: -1.34 (0.18), residues: 774 loop : -1.39 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 361 TYR 0.020 0.002 TYR A 381 PHE 0.024 0.001 PHE F 595 TRP 0.009 0.001 TRP B 651 HIS 0.011 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00292 (31266) covalent geometry : angle 0.55503 (42438) hydrogen bonds : bond 0.03046 ( 1267) hydrogen bonds : angle 4.79276 ( 3777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 329 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8231 (pt) REVERT: A 567 MET cc_start: 0.9250 (mmp) cc_final: 0.8968 (mmm) REVERT: B 26 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7823 (mm) REVERT: B 120 ASP cc_start: 0.8424 (t0) cc_final: 0.8045 (t0) REVERT: B 221 HIS cc_start: 0.8508 (m-70) cc_final: 0.8212 (m-70) REVERT: B 293 GLN cc_start: 0.8261 (mt0) cc_final: 0.7947 (mt0) REVERT: B 414 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: B 437 GLN cc_start: 0.8310 (mt0) cc_final: 0.7886 (mp10) REVERT: B 567 MET cc_start: 0.8506 (mmm) cc_final: 0.8208 (mmm) REVERT: C 20 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7080 (ttm170) REVERT: C 33 GLU cc_start: 0.7214 (pp20) cc_final: 0.6953 (pp20) REVERT: C 351 ASN cc_start: 0.8661 (m-40) cc_final: 0.8451 (m-40) REVERT: C 551 ASP cc_start: 0.8688 (m-30) cc_final: 0.8341 (m-30) REVERT: D 33 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8030 (pp20) REVERT: D 120 ASP cc_start: 0.8452 (t0) cc_final: 0.8132 (t0) REVERT: D 127 ASP cc_start: 0.7882 (m-30) cc_final: 0.7638 (m-30) REVERT: D 164 MET cc_start: 0.9107 (ttt) cc_final: 0.8874 (ttp) REVERT: D 223 ASP cc_start: 0.7827 (t0) cc_final: 0.7344 (t0) REVERT: D 345 ASP cc_start: 0.7245 (m-30) cc_final: 0.7008 (m-30) REVERT: D 433 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7979 (mm-40) REVERT: D 504 THR cc_start: 0.9382 (t) cc_final: 0.8990 (m) REVERT: D 610 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7687 (tp30) REVERT: D 616 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: E 33 GLU cc_start: 0.7302 (pp20) cc_final: 0.6963 (pp20) REVERT: E 78 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8310 (pp20) REVERT: E 122 THR cc_start: 0.8950 (m) cc_final: 0.8648 (p) REVERT: E 135 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 205 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6475 (pp20) REVERT: E 220 ASP cc_start: 0.8875 (m-30) cc_final: 0.8381 (m-30) REVERT: E 243 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: F 78 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: F 120 ASP cc_start: 0.8504 (t0) cc_final: 0.8054 (t0) REVERT: F 293 GLN cc_start: 0.8286 (mt0) cc_final: 0.7959 (mt0) REVERT: F 404 MET cc_start: 0.9394 (ptp) cc_final: 0.9119 (ptp) REVERT: F 414 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: F 504 THR cc_start: 0.9186 (t) cc_final: 0.8834 (m) REVERT: F 505 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9078 (mmm) REVERT: F 616 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8021 (tt0) REVERT: F 632 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8507 (ttt180) outliers start: 104 outliers final: 41 residues processed: 406 average time/residue: 0.7397 time to fit residues: 347.2174 Evaluate side-chains 334 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 386 ASP Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 299 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 161 optimal weight: 0.0980 chunk 324 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 239 optimal weight: 0.8980 chunk 372 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 HIS A 450 GLN A 659 HIS B 158 ASN C 24 HIS C 46 GLN D 347 GLN D 411 HIS D 472 HIS E 320 GLN E 411 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091645 restraints weight = 43525.671| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.85 r_work: 0.2918 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31266 Z= 0.127 Angle : 0.556 9.565 42438 Z= 0.281 Chirality : 0.042 0.147 4836 Planarity : 0.004 0.040 5568 Dihedral : 4.418 20.503 4334 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.96 % Allowed : 16.38 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.13), residues: 4056 helix: 0.57 (0.14), residues: 1446 sheet: -1.25 (0.19), residues: 774 loop : -1.36 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 444 TYR 0.018 0.002 TYR E 607 PHE 0.024 0.001 PHE E 595 TRP 0.008 0.001 TRP E 651 HIS 0.021 0.001 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00291 (31266) covalent geometry : angle 0.55581 (42438) hydrogen bonds : bond 0.02996 ( 1267) hydrogen bonds : angle 4.70855 ( 3777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 312 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8697 (mm) REVERT: A 524 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8226 (pt) REVERT: A 567 MET cc_start: 0.9253 (mmp) cc_final: 0.8968 (mmm) REVERT: B 26 ILE cc_start: 0.8102 (OUTLIER) cc_final: 0.7872 (mm) REVERT: B 120 ASP cc_start: 0.8391 (t0) cc_final: 0.8031 (t0) REVERT: B 287 MET cc_start: 0.8291 (mtp) cc_final: 0.8065 (mtp) REVERT: B 348 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: B 414 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8030 (mt0) REVERT: B 437 GLN cc_start: 0.8274 (mt0) cc_final: 0.7899 (mp10) REVERT: B 567 MET cc_start: 0.8492 (mmm) cc_final: 0.8189 (mmm) REVERT: C 20 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.7029 (ttm170) REVERT: C 33 GLU cc_start: 0.7229 (pp20) cc_final: 0.6961 (pp20) REVERT: C 351 ASN cc_start: 0.8654 (m-40) cc_final: 0.8426 (m-40) REVERT: C 459 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: D 120 ASP cc_start: 0.8454 (t0) cc_final: 0.8125 (t0) REVERT: D 127 ASP cc_start: 0.7867 (m-30) cc_final: 0.7599 (m-30) REVERT: D 164 MET cc_start: 0.9126 (ttt) cc_final: 0.8741 (ttp) REVERT: D 223 ASP cc_start: 0.7854 (t0) cc_final: 0.7375 (t0) REVERT: D 345 ASP cc_start: 0.7381 (m-30) cc_final: 0.7137 (m-30) REVERT: D 433 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7764 (mm110) REVERT: D 437 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7485 (mt0) REVERT: D 504 THR cc_start: 0.9397 (t) cc_final: 0.8985 (m) REVERT: D 610 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7674 (tp30) REVERT: D 616 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8557 (tt0) REVERT: E 33 GLU cc_start: 0.7247 (pp20) cc_final: 0.6886 (pp20) REVERT: E 78 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8320 (pp20) REVERT: E 122 THR cc_start: 0.8944 (m) cc_final: 0.8634 (p) REVERT: E 135 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: E 205 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6533 (pp20) REVERT: E 220 ASP cc_start: 0.8876 (m-30) cc_final: 0.8380 (m-30) REVERT: E 243 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7763 (tm-30) REVERT: F 78 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: F 120 ASP cc_start: 0.8488 (t0) cc_final: 0.8029 (t0) REVERT: F 293 GLN cc_start: 0.8307 (mt0) cc_final: 0.7946 (mt0) REVERT: F 404 MET cc_start: 0.9388 (ptp) cc_final: 0.9063 (ptp) REVERT: F 414 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: F 490 VAL cc_start: 0.9157 (OUTLIER) cc_final: 0.8957 (t) REVERT: F 504 THR cc_start: 0.9199 (t) cc_final: 0.8858 (m) REVERT: F 505 MET cc_start: 0.9367 (tpt) cc_final: 0.9059 (mmm) REVERT: F 616 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8054 (tt0) outliers start: 94 outliers final: 44 residues processed: 383 average time/residue: 0.7553 time to fit residues: 333.9701 Evaluate side-chains 352 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 291 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 348 GLU Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 547 MET Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 379 optimal weight: 0.4980 chunk 392 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 191 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 388 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 376 optimal weight: 0.9990 chunk 252 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 HIS B 433 GLN D 3 GLN D 347 GLN D 411 HIS E 46 GLN E 245 ASN E 411 HIS F 469 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.088410 restraints weight = 43555.333| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.84 r_work: 0.2868 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31266 Z= 0.213 Angle : 0.619 11.418 42438 Z= 0.313 Chirality : 0.045 0.152 4836 Planarity : 0.005 0.042 5568 Dihedral : 4.631 21.949 4334 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.25 % Allowed : 16.76 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 4056 helix: 0.50 (0.14), residues: 1476 sheet: -1.23 (0.19), residues: 774 loop : -1.30 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 281 TYR 0.021 0.002 TYR A 381 PHE 0.024 0.002 PHE C 595 TRP 0.011 0.001 TRP A 124 HIS 0.017 0.001 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00499 (31266) covalent geometry : angle 0.61891 (42438) hydrogen bonds : bond 0.03426 ( 1267) hydrogen bonds : angle 4.87036 ( 3777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 294 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8730 (mm) REVERT: A 33 GLU cc_start: 0.7625 (pp20) cc_final: 0.6250 (pp20) REVERT: A 122 THR cc_start: 0.8877 (m) cc_final: 0.8635 (p) REVERT: A 515 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7484 (tpt-90) REVERT: A 524 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8329 (pt) REVERT: A 567 MET cc_start: 0.9270 (mmp) cc_final: 0.8857 (mmp) REVERT: B 26 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8011 (mm) REVERT: B 33 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: B 120 ASP cc_start: 0.8498 (t0) cc_final: 0.8146 (t0) REVERT: B 287 MET cc_start: 0.8448 (mtp) cc_final: 0.8189 (mtp) REVERT: B 414 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8054 (mt0) REVERT: B 437 GLN cc_start: 0.8320 (mt0) cc_final: 0.7943 (mp10) REVERT: B 549 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7787 (tt0) REVERT: C 20 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7094 (ttm170) REVERT: C 33 GLU cc_start: 0.7352 (pp20) cc_final: 0.6983 (pp20) REVERT: C 351 ASN cc_start: 0.8689 (m-40) cc_final: 0.8470 (m-40) REVERT: C 459 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7437 (pt0) REVERT: D 120 ASP cc_start: 0.8581 (t0) cc_final: 0.8237 (t0) REVERT: D 223 ASP cc_start: 0.7974 (t0) cc_final: 0.7640 (t0) REVERT: D 318 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8219 (ttm-80) REVERT: D 345 ASP cc_start: 0.7389 (m-30) cc_final: 0.7148 (m-30) REVERT: D 433 GLN cc_start: 0.8355 (mm-40) cc_final: 0.7834 (mm-40) REVERT: D 437 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7506 (mt0) REVERT: D 610 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7779 (tp30) REVERT: D 616 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: E 33 GLU cc_start: 0.7335 (pp20) cc_final: 0.6995 (pp20) REVERT: E 78 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8387 (pp20) REVERT: E 122 THR cc_start: 0.9022 (m) cc_final: 0.8759 (p) REVERT: E 135 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: E 205 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6513 (pp20) REVERT: E 220 ASP cc_start: 0.8892 (m-30) cc_final: 0.8560 (m-30) REVERT: E 243 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7831 (tm-30) REVERT: E 522 ASP cc_start: 0.7701 (p0) cc_final: 0.7387 (p0) REVERT: E 606 ASN cc_start: 0.8558 (OUTLIER) cc_final: 0.8116 (t0) REVERT: F 78 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7640 (pp20) REVERT: F 120 ASP cc_start: 0.8600 (t0) cc_final: 0.8150 (t0) REVERT: F 293 GLN cc_start: 0.8440 (mt0) cc_final: 0.8077 (mt0) REVERT: F 345 ASP cc_start: 0.7201 (m-30) cc_final: 0.6999 (m-30) REVERT: F 404 MET cc_start: 0.9400 (ptp) cc_final: 0.9129 (ptp) REVERT: F 414 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: F 504 THR cc_start: 0.9210 (t) cc_final: 0.8771 (m) REVERT: F 616 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8178 (tt0) outliers start: 103 outliers final: 44 residues processed: 373 average time/residue: 0.7769 time to fit residues: 333.7025 Evaluate side-chains 336 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 437 GLN Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 116 ARG Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 606 ASN Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 487 LEU Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 386 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 208 optimal weight: 4.9990 chunk 331 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 265 optimal weight: 0.0000 chunk 29 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 GLN B 3 GLN B 221 HIS B 433 GLN C 339 ASN D 347 GLN D 411 HIS E 411 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.117519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.091557 restraints weight = 43621.422| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.85 r_work: 0.2902 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31266 Z= 0.121 Angle : 0.557 9.120 42438 Z= 0.282 Chirality : 0.042 0.150 4836 Planarity : 0.004 0.040 5568 Dihedral : 4.387 19.476 4334 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.55 % Allowed : 17.27 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4056 helix: 0.75 (0.14), residues: 1446 sheet: -1.18 (0.19), residues: 774 loop : -1.24 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 361 TYR 0.020 0.002 TYR E 607 PHE 0.023 0.001 PHE E 595 TRP 0.009 0.001 TRP D 97 HIS 0.016 0.001 HIS E 463 Details of bonding type rmsd covalent geometry : bond 0.00276 (31266) covalent geometry : angle 0.55651 (42438) hydrogen bonds : bond 0.02940 ( 1267) hydrogen bonds : angle 4.67543 ( 3777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 307 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8704 (mm) REVERT: A 33 GLU cc_start: 0.7676 (pp20) cc_final: 0.7347 (pp20) REVERT: A 515 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.7103 (tpt-90) REVERT: A 524 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8202 (pt) REVERT: A 567 MET cc_start: 0.9265 (mmp) cc_final: 0.8719 (mmp) REVERT: B 33 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8235 (pp20) REVERT: B 120 ASP cc_start: 0.8415 (t0) cc_final: 0.8053 (t0) REVERT: B 361 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7287 (ttt90) REVERT: B 414 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: B 437 GLN cc_start: 0.8295 (mt0) cc_final: 0.7917 (mp10) REVERT: B 549 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: C 20 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7044 (ttm170) REVERT: C 33 GLU cc_start: 0.7262 (pp20) cc_final: 0.6912 (pp20) REVERT: C 83 TYR cc_start: 0.8615 (m-80) cc_final: 0.8390 (m-80) REVERT: C 330 GLU cc_start: 0.7569 (mp0) cc_final: 0.7254 (mm-30) REVERT: C 351 ASN cc_start: 0.8616 (m-40) cc_final: 0.8399 (m-40) REVERT: C 459 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: C 551 ASP cc_start: 0.8651 (m-30) cc_final: 0.8418 (m-30) REVERT: D 33 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8248 (pp20) REVERT: D 120 ASP cc_start: 0.8531 (t0) cc_final: 0.8193 (t0) REVERT: D 127 ASP cc_start: 0.7886 (m-30) cc_final: 0.7603 (m-30) REVERT: D 223 ASP cc_start: 0.7875 (t0) cc_final: 0.7393 (t0) REVERT: D 318 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: D 345 ASP cc_start: 0.7295 (m-30) cc_final: 0.7070 (m-30) REVERT: D 433 GLN cc_start: 0.8321 (mm-40) cc_final: 0.7885 (mm110) REVERT: D 610 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7704 (tp30) REVERT: D 616 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8577 (tt0) REVERT: E 33 GLU cc_start: 0.7205 (pp20) cc_final: 0.6931 (pp20) REVERT: E 78 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8363 (pp20) REVERT: E 122 THR cc_start: 0.8976 (m) cc_final: 0.8704 (p) REVERT: E 135 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: E 205 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6452 (pp20) REVERT: E 220 ASP cc_start: 0.8823 (m-30) cc_final: 0.8477 (m-30) REVERT: E 243 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: F 78 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7558 (pp20) REVERT: F 120 ASP cc_start: 0.8511 (t0) cc_final: 0.8038 (t0) REVERT: F 293 GLN cc_start: 0.8299 (mt0) cc_final: 0.7998 (mt0) REVERT: F 414 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: F 504 THR cc_start: 0.9223 (t) cc_final: 0.8858 (m) REVERT: F 505 MET cc_start: 0.9367 (OUTLIER) cc_final: 0.9098 (mmm) REVERT: F 616 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8145 (tt0) REVERT: F 639 ARG cc_start: 0.7602 (pmm150) cc_final: 0.7214 (pmm-80) REVERT: F 642 GLU cc_start: 0.7465 (pm20) cc_final: 0.6830 (pp20) outliers start: 81 outliers final: 38 residues processed: 371 average time/residue: 0.7722 time to fit residues: 330.2292 Evaluate side-chains 336 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 280 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 549 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 26 optimal weight: 6.9990 chunk 114 optimal weight: 0.0470 chunk 28 optimal weight: 4.9990 chunk 291 optimal weight: 7.9990 chunk 266 optimal weight: 0.0050 chunk 279 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 284 optimal weight: 0.6980 chunk 308 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 0.7294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 ASN B 221 HIS C 500 GLN D 347 GLN D 411 HIS F 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091649 restraints weight = 43625.896| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.85 r_work: 0.2935 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31266 Z= 0.127 Angle : 0.561 9.973 42438 Z= 0.284 Chirality : 0.042 0.154 4836 Planarity : 0.004 0.040 5568 Dihedral : 4.340 19.743 4334 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.14 % Allowed : 18.02 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.13), residues: 4056 helix: 0.89 (0.14), residues: 1464 sheet: -1.11 (0.19), residues: 774 loop : -1.10 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 444 TYR 0.020 0.002 TYR A 381 PHE 0.023 0.001 PHE E 595 TRP 0.012 0.001 TRP D 97 HIS 0.019 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00290 (31266) covalent geometry : angle 0.56056 (42438) hydrogen bonds : bond 0.02938 ( 1267) hydrogen bonds : angle 4.64226 ( 3777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 299 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8704 (mm) REVERT: A 33 GLU cc_start: 0.7699 (pp20) cc_final: 0.7446 (pp20) REVERT: A 320 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: A 515 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7067 (tpt-90) REVERT: A 524 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8191 (pt) REVERT: A 567 MET cc_start: 0.9276 (mmp) cc_final: 0.8720 (mmp) REVERT: B 33 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8266 (pp20) REVERT: B 120 ASP cc_start: 0.8397 (t0) cc_final: 0.8033 (t0) REVERT: B 437 GLN cc_start: 0.8289 (mt0) cc_final: 0.7979 (mp10) REVERT: C 20 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7060 (ttm170) REVERT: C 33 GLU cc_start: 0.7263 (pp20) cc_final: 0.6916 (pp20) REVERT: C 330 GLU cc_start: 0.7490 (mp0) cc_final: 0.7146 (mm-30) REVERT: C 351 ASN cc_start: 0.8646 (m-40) cc_final: 0.8434 (m-40) REVERT: C 459 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7435 (pt0) REVERT: C 551 ASP cc_start: 0.8660 (m-30) cc_final: 0.8424 (m-30) REVERT: C 650 GLU cc_start: 0.8814 (tt0) cc_final: 0.8591 (tt0) REVERT: D 33 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8299 (pp20) REVERT: D 120 ASP cc_start: 0.8516 (t0) cc_final: 0.8180 (t0) REVERT: D 127 ASP cc_start: 0.7876 (m-30) cc_final: 0.7584 (m-30) REVERT: D 223 ASP cc_start: 0.7886 (t0) cc_final: 0.7666 (t0) REVERT: D 318 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8074 (ttm-80) REVERT: D 345 ASP cc_start: 0.7330 (m-30) cc_final: 0.7104 (m-30) REVERT: D 433 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7921 (mm110) REVERT: D 616 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: E 33 GLU cc_start: 0.7239 (pp20) cc_final: 0.6908 (pp20) REVERT: E 78 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8401 (pp20) REVERT: E 122 THR cc_start: 0.8952 (m) cc_final: 0.8687 (p) REVERT: E 135 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: E 205 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6601 (pp20) REVERT: E 220 ASP cc_start: 0.8819 (m-30) cc_final: 0.8495 (m-30) REVERT: E 243 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7835 (tm-30) REVERT: E 629 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8974 (t) REVERT: F 78 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7580 (pp20) REVERT: F 120 ASP cc_start: 0.8548 (t0) cc_final: 0.8116 (t0) REVERT: F 293 GLN cc_start: 0.8350 (mt0) cc_final: 0.7987 (mt0) REVERT: F 404 MET cc_start: 0.9381 (ptp) cc_final: 0.9033 (ptp) REVERT: F 414 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8043 (mt0) REVERT: F 504 THR cc_start: 0.9224 (t) cc_final: 0.8871 (m) REVERT: F 505 MET cc_start: 0.9369 (OUTLIER) cc_final: 0.9092 (mmm) REVERT: F 616 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: F 639 ARG cc_start: 0.7511 (pmm150) cc_final: 0.7137 (pmm-80) REVERT: F 642 GLU cc_start: 0.7465 (pm20) cc_final: 0.6819 (pp20) outliers start: 68 outliers final: 42 residues processed: 350 average time/residue: 0.7547 time to fit residues: 304.5797 Evaluate side-chains 341 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 515 ARG Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 616 GLU Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 135 GLU Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 524 ILE Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 240 optimal weight: 0.6980 chunk 202 optimal weight: 7.9990 chunk 172 optimal weight: 0.2980 chunk 113 optimal weight: 0.0040 chunk 234 optimal weight: 6.9990 chunk 299 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 362 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 9 optimal weight: 2.9990 chunk 391 optimal weight: 0.9980 overall best weight: 0.4150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 HIS B 221 HIS B 433 GLN C 500 GLN D 347 GLN D 411 HIS F 469 GLN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.119541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.094336 restraints weight = 43492.220| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.76 r_work: 0.2984 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31266 Z= 0.105 Angle : 0.540 9.132 42438 Z= 0.274 Chirality : 0.042 0.139 4836 Planarity : 0.004 0.040 5568 Dihedral : 4.182 18.759 4334 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.02 % Allowed : 18.37 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4056 helix: 1.03 (0.14), residues: 1470 sheet: -0.98 (0.19), residues: 720 loop : -1.09 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 361 TYR 0.020 0.001 TYR E 607 PHE 0.023 0.001 PHE F 595 TRP 0.015 0.001 TRP D 97 HIS 0.017 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00237 (31266) covalent geometry : angle 0.53960 (42438) hydrogen bonds : bond 0.02724 ( 1267) hydrogen bonds : angle 4.51550 ( 3777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8112 Ramachandran restraints generated. 4056 Oldfield, 0 Emsley, 4056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 317 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7677 (pp20) cc_final: 0.7443 (pp20) REVERT: A 320 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: A 504 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8863 (m) REVERT: A 524 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8025 (pt) REVERT: A 567 MET cc_start: 0.9278 (mmp) cc_final: 0.8738 (mmp) REVERT: A 610 GLU cc_start: 0.7977 (tp30) cc_final: 0.7659 (tp30) REVERT: B 33 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8153 (pp20) REVERT: B 120 ASP cc_start: 0.8365 (t0) cc_final: 0.8031 (t0) REVERT: B 437 GLN cc_start: 0.8232 (mt0) cc_final: 0.7962 (mp10) REVERT: B 504 THR cc_start: 0.9275 (OUTLIER) cc_final: 0.8673 (m) REVERT: C 20 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7016 (ttm170) REVERT: C 33 GLU cc_start: 0.7081 (pp20) cc_final: 0.6787 (pp20) REVERT: C 330 GLU cc_start: 0.7469 (mp0) cc_final: 0.7138 (mm-30) REVERT: C 351 ASN cc_start: 0.8567 (m-40) cc_final: 0.8358 (m-40) REVERT: C 459 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: C 551 ASP cc_start: 0.8670 (m-30) cc_final: 0.8429 (m-30) REVERT: C 629 THR cc_start: 0.9292 (OUTLIER) cc_final: 0.9072 (t) REVERT: C 650 GLU cc_start: 0.8828 (tt0) cc_final: 0.8553 (tt0) REVERT: D 33 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8188 (pp20) REVERT: D 120 ASP cc_start: 0.8459 (t0) cc_final: 0.8132 (t0) REVERT: D 223 ASP cc_start: 0.7808 (t0) cc_final: 0.7598 (t0) REVERT: D 318 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8100 (ttm-80) REVERT: D 345 ASP cc_start: 0.7321 (m-30) cc_final: 0.7092 (m-30) REVERT: D 374 PHE cc_start: 0.8758 (m-80) cc_final: 0.8508 (m-80) REVERT: D 433 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7801 (mm-40) REVERT: E 33 GLU cc_start: 0.7183 (pp20) cc_final: 0.6890 (pp20) REVERT: E 122 THR cc_start: 0.8861 (m) cc_final: 0.8601 (p) REVERT: E 220 ASP cc_start: 0.8729 (m-30) cc_final: 0.8400 (m-30) REVERT: E 243 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: E 629 THR cc_start: 0.9207 (OUTLIER) cc_final: 0.8859 (m) REVERT: F 78 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: F 120 ASP cc_start: 0.8497 (t0) cc_final: 0.8098 (t0) REVERT: F 293 GLN cc_start: 0.8261 (mt0) cc_final: 0.7742 (mt0) REVERT: F 404 MET cc_start: 0.9341 (ptp) cc_final: 0.9004 (ptp) REVERT: F 504 THR cc_start: 0.9175 (t) cc_final: 0.8863 (m) REVERT: F 505 MET cc_start: 0.9343 (OUTLIER) cc_final: 0.9081 (mmm) REVERT: F 616 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: F 639 ARG cc_start: 0.7420 (pmm150) cc_final: 0.7033 (pmm-80) REVERT: F 642 GLU cc_start: 0.7384 (pm20) cc_final: 0.6750 (pp20) outliers start: 64 outliers final: 37 residues processed: 368 average time/residue: 0.7572 time to fit residues: 321.5725 Evaluate side-chains 346 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 295 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 GLN Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 648 VAL Chi-restraints excluded: chain B residue 656 PHE Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 459 GLU Chi-restraints excluded: chain C residue 490 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 596 VAL Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 307 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 471 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 676 HIS Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 243 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 490 VAL Chi-restraints excluded: chain E residue 504 THR Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain F residue 433 GLN Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 505 MET Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Chi-restraints excluded: chain F residue 632 ARG Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 656 PHE Chi-restraints excluded: chain F residue 676 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 215 optimal weight: 4.9990 chunk 341 optimal weight: 2.9990 chunk 358 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 312 optimal weight: 3.9990 chunk 231 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 372 optimal weight: 0.8980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN B 433 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 676 HIS ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 HIS E 409 GLN ** E 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.088478 restraints weight = 43879.324| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.84 r_work: 0.2841 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 31266 Z= 0.226 Angle : 0.637 9.460 42438 Z= 0.322 Chirality : 0.046 0.260 4836 Planarity : 0.005 0.042 5568 Dihedral : 4.513 21.533 4334 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.17 % Allowed : 18.68 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4056 helix: 0.79 (0.14), residues: 1470 sheet: -1.06 (0.19), residues: 762 loop : -1.08 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 361 TYR 0.024 0.002 TYR F 607 PHE 0.024 0.002 PHE C 595 TRP 0.024 0.002 TRP D 97 HIS 0.017 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00530 (31266) covalent geometry : angle 0.63694 (42438) hydrogen bonds : bond 0.03430 ( 1267) hydrogen bonds : angle 4.77977 ( 3777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10199.71 seconds wall clock time: 174 minutes 20.92 seconds (10460.92 seconds total)