Starting phenix.real_space_refine on Fri Mar 6 12:32:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jqm_9874/03_2026/6jqm_9874.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jqm_9874/03_2026/6jqm_9874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6jqm_9874/03_2026/6jqm_9874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jqm_9874/03_2026/6jqm_9874.map" model { file = "/net/cci-nas-00/data/ceres_data/6jqm_9874/03_2026/6jqm_9874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jqm_9874/03_2026/6jqm_9874.cif" } resolution = 3.3 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 150 5.16 5 C 19470 2.51 5 N 5466 2.21 5 O 5832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 30936 Number of models: 1 Model: "" Number of chains: 12 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} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.62, per 1000 atoms: 0.21 Number of scatterers: 30936 At special positions: 0 Unit cell: (179.14, 174.9, 108.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 150 16.00 P 18 15.00 O 5832 8.00 N 5466 7.00 C 19470 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: 2.16 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: 137 helices and 46 sheets defined 37.2% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 40 through 58 removed outlier: 3.601A pdb=" N ALA A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG A 45 " --> pdb=" O MET A 41 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.503A pdb=" N LEU A 68 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.635A pdb=" N TYR A 83 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) 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 115 removed outlier: 3.677A pdb=" N VAL A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 174 removed outlier: 4.153A pdb=" N LYS A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 186 through 199 removed outlier: 4.217A pdb=" N THR A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 removed outlier: 3.529A pdb=" N MET A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 273 through 289 removed outlier: 4.463A pdb=" N ALA A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 278 " --> pdb=" O PRO A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 293 Processing helix chain 'A' and resid 307 through 320 removed outlier: 3.571A pdb=" N ALA A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.586A pdb=" N LYS A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 3.530A pdb=" N GLN A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 443 removed outlier: 3.662A pdb=" N ALA A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 437 " --> pdb=" O GLN A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 502 through 510 removed outlier: 4.061A pdb=" N ALA A 508 " --> pdb=" O THR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 534 removed outlier: 3.599A pdb=" N GLU A 533 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 560 removed outlier: 3.843A pdb=" N ILE A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 Processing helix chain 'A' and resid 568 through 575 removed outlier: 3.647A pdb=" N ALA A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 596 removed outlier: 3.632A pdb=" N ALA A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 51 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.565A pdb=" N LEU B 68 " --> pdb=" O ARG B 64 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.584A pdb=" N TYR B 83 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) 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: 3.975A pdb=" N VAL B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 174 removed outlier: 3.633A pdb=" N MET B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) removed outlier: 3.711A 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: 4.090A pdb=" N THR B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 4.166A pdb=" N LEU B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.580A pdb=" N MET B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 273 through 289 removed outlier: 4.048A 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 Processing helix chain 'B' and resid 339 through 355 removed outlier: 3.636A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.767A pdb=" N GLN B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 removed outlier: 3.606A pdb=" N ALA B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 3.543A 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 492 removed outlier: 3.904A pdb=" N ALA B 489 " --> pdb=" O GLY B 486 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 490 " --> pdb=" O LEU B 487 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B 491 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.128A pdb=" N ALA B 508 " --> pdb=" O THR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 560 Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 583 through 596 removed outlier: 3.643A pdb=" N ALA B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 58 removed outlier: 3.836A pdb=" N ALA C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Proline residue: C 54 - end of helix Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.596A pdb=" N LEU C 68 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 87 removed outlier: 3.614A pdb=" N TYR C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) 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 118 removed outlier: 3.808A pdb=" N VAL C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 107 " --> pdb=" O GLY C 103 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 174 removed outlier: 4.206A pdb=" N LYS C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) removed outlier: 3.717A 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: 4.206A pdb=" N THR C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 242 removed outlier: 3.665A pdb=" N MET C 239 " --> pdb=" O ALA C 235 " (cutoff:3.500A) removed outlier: 3.515A 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: 4.429A 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: 3.847A pdb=" N ASP C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 316 " --> pdb=" O SER C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 355 removed outlier: 3.519A pdb=" N LYS C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 352 " --> pdb=" O GLU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.741A pdb=" N GLN C 414 " --> pdb=" O ARG C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 443 removed outlier: 3.709A pdb=" N ALA C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG C 436 " --> pdb=" O PRO C 432 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 437 " --> pdb=" O GLN C 433 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 502 through 510 removed outlier: 4.015A pdb=" N ALA C 508 " --> pdb=" O THR C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 560 removed outlier: 3.877A pdb=" N ILE C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 583 through 596 removed outlier: 3.621A pdb=" N ALA C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 596 " --> pdb=" O ALA C 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 51 Processing helix chain 'D' and resid 52 through 58 Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.786A pdb=" N GLU D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 3.609A pdb=" N TYR D 83 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) 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 118 removed outlier: 3.847A pdb=" N VAL D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU D 107 " --> pdb=" O GLY D 103 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 167 through 174 removed outlier: 3.532A pdb=" N THR D 171 " --> pdb=" O LYS D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 199 removed outlier: 4.213A pdb=" N THR D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.968A pdb=" N LEU D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 3.505A pdb=" N GLY D 237 " --> pdb=" O SER D 233 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET D 239 " --> pdb=" O ALA D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 273 through 289 removed outlier: 3.990A 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 Processing helix chain 'D' and resid 339 through 355 removed outlier: 3.662A pdb=" N ILE D 352 " --> pdb=" O GLU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 418 removed outlier: 3.759A pdb=" N GLN D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 443 removed outlier: 3.827A pdb=" N ALA D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG D 436 " --> pdb=" O PRO D 432 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN D 437 " --> pdb=" O GLN D 433 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP D 441 " --> pdb=" O GLN D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 489 through 492 removed outlier: 3.595A pdb=" N HIS D 492 " --> pdb=" O ALA D 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 489 through 492' Processing helix chain 'D' and resid 502 through 511 removed outlier: 4.041A 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 548 through 560 Processing helix chain 'D' and resid 563 through 568 Processing helix chain 'D' and resid 568 through 573 removed outlier: 3.673A pdb=" N ALA D 572 " --> pdb=" O ASP D 568 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 573 " --> pdb=" O LYS D 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 568 through 573' Processing helix chain 'D' and resid 583 through 596 removed outlier: 3.555A pdb=" N ALA D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 52 Processing helix chain 'E' and resid 52 through 58 Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.551A pdb=" N LEU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 87 removed outlier: 3.548A pdb=" N TYR E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU E 85 " --> pdb=" O ARG E 81 " (cutoff:3.500A) 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 118 removed outlier: 3.686A pdb=" N VAL E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 107 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU E 118 " --> pdb=" O GLY E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 174 removed outlier: 4.287A pdb=" N LYS E 167 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Proline residue: E 170 - end of helix Processing helix chain 'E' and resid 186 through 199 removed outlier: 4.258A pdb=" N THR E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 242 removed outlier: 3.728A pdb=" N MET E 239 " --> pdb=" O ALA E 235 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 289 removed outlier: 4.378A 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: 3.741A pdb=" N ASP E 313 " --> pdb=" O ASN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 355 removed outlier: 3.544A pdb=" N LYS E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 418 removed outlier: 3.718A pdb=" N GLN E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 443 removed outlier: 3.578A pdb=" N ALA E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP E 441 " --> pdb=" O GLN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 489 through 492 Processing helix chain 'E' and resid 502 through 510 removed outlier: 3.914A pdb=" N ALA E 508 " --> pdb=" O THR E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 529 Processing helix chain 'E' and resid 548 through 560 removed outlier: 3.777A pdb=" N ILE E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 568 through 575 removed outlier: 3.581A pdb=" N ALA E 572 " --> pdb=" O ASP E 568 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 573 " --> pdb=" O LYS E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 596 removed outlier: 3.714A pdb=" N ALA E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 51 Processing helix chain 'F' and resid 52 through 58 Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.576A pdb=" N LEU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU F 78 " --> pdb=" O HIS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 87 removed outlier: 3.900A pdb=" N ALA F 84 " --> pdb=" O GLU F 80 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU F 85 " --> pdb=" O ARG F 81 " (cutoff:3.500A) 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 118 removed outlier: 3.868A pdb=" N VAL F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP F 99 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 118 " --> pdb=" O GLY F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 166 removed outlier: 3.754A pdb=" N MET F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 removed outlier: 3.647A pdb=" N THR F 171 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 199 removed outlier: 4.179A pdb=" N THR F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 241 removed outlier: 3.830A pdb=" N MET F 239 " --> pdb=" O ALA F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 250 Processing helix chain 'F' and resid 273 through 289 removed outlier: 3.949A 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: 3.884A pdb=" N VAL F 316 " --> pdb=" O SER F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 355 removed outlier: 3.590A pdb=" N ILE F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 418 removed outlier: 3.684A pdb=" N GLN F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 443 removed outlier: 3.847A pdb=" N ALA F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG F 436 " --> pdb=" O PRO F 432 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN F 437 " --> pdb=" O GLN F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 489 through 492 removed outlier: 3.507A pdb=" N HIS F 492 " --> pdb=" O ALA F 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 489 through 492' Processing helix chain 'F' and resid 502 through 510 removed outlier: 4.071A pdb=" N ALA F 508 " --> pdb=" O THR F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 560 Processing helix chain 'F' and resid 570 through 574 Processing helix chain 'F' and resid 583 through 596 removed outlier: 3.547A pdb=" N VAL F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) 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 removed outlier: 3.663A pdb=" N TRP A 32 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 125 removed outlier: 3.690A pdb=" N ILE B 451 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY B 425 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU B 452 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 427 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN B 261 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG B 299 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N MET B 404 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 301 " --> pdb=" O MET B 404 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA B 406 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL B 303 " --> pdb=" O ALA B 406 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 378 " --> pdb=" O ALA B 401 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LEU B 403 " --> pdb=" O THR B 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 6.591A pdb=" N ALA A 151 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS A 181 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS A 153 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.762A pdb=" N THR A 378 " --> pdb=" O ALA A 401 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N LEU A 403 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ARG A 299 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 261 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY A 425 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU A 452 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 427 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.815A 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 removed outlier: 3.541A pdb=" N ASP A 622 " --> pdb=" O MET A 547 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 541 removed outlier: 6.502A pdb=" N GLU A 650 " --> pdb=" O LYS A 631 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 655 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA A 664 " --> pdb=" O VAL A 655 " (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 3 through 4 removed outlier: 3.710A pdb=" N TRP B 32 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 6 through 8 Processing sheet with id=AB4, first strand: chain 'B' and resid 208 through 210 removed outlier: 6.347A pdb=" N ALA B 151 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS B 181 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS B 153 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 545 through 547 removed outlier: 6.442A pdb=" N GLU B 650 " --> pdb=" O LYS B 631 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 671 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB7, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.772A pdb=" N TRP C 32 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'C' and resid 208 through 210 removed outlier: 6.437A pdb=" N ALA C 151 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS C 181 " --> pdb=" O ALA C 151 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N HIS C 153 " --> pdb=" O LYS C 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 358 through 359 removed outlier: 3.992A pdb=" N TYR C 381 " --> pdb=" O CYS C 358 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR C 378 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU C 403 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU C 380 " --> pdb=" O LEU C 403 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG C 299 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N MET C 404 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE C 301 " --> pdb=" O MET C 404 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA C 406 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL C 303 " --> pdb=" O ALA C 406 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN C 261 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY C 425 " --> pdb=" O GLN C 450 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 452 " --> pdb=" O GLY C 425 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU C 427 " --> pdb=" O LEU C 452 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE C 449 " --> pdb=" O GLN D 500 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.865A pdb=" N ALA C 605 " --> pdb=" O LEU C 671 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA C 673 " --> pdb=" O VAL C 603 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL C 603 " --> pdb=" O ALA C 673 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 545 through 547 removed outlier: 3.569A pdb=" N ASP C 622 " --> pdb=" O MET C 547 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL C 655 " --> pdb=" O ALA C 664 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA C 664 " --> pdb=" O VAL C 655 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 608 through 609 Processing sheet with id=AC5, first strand: chain 'C' and resid 612 through 613 Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 4 removed outlier: 3.623A pdb=" N TRP D 32 " --> pdb=" O ILE D 22 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AC8, first strand: chain 'D' and resid 208 through 210 removed outlier: 6.381A pdb=" N ALA D 151 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS D 181 " --> pdb=" O ALA D 151 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N HIS D 153 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 378 through 379 removed outlier: 6.694A pdb=" N THR D 378 " --> pdb=" O ALA D 401 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N LEU D 403 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG D 299 " --> pdb=" O THR D 402 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N MET D 404 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 301 " --> pdb=" O MET D 404 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ALA D 406 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL D 303 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASN D 261 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY D 425 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU D 452 " --> pdb=" O GLY D 425 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU D 427 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 540 through 541 Processing sheet with id=AD2, first strand: chain 'D' and resid 540 through 541 Processing sheet with id=AD3, first strand: chain 'D' and resid 630 through 632 Processing sheet with id=AD4, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AD5, first strand: chain 'E' and resid 20 through 23 removed outlier: 3.723A pdb=" N TRP E 32 " --> pdb=" O ILE E 22 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 124 through 125 removed outlier: 3.573A pdb=" N TRP E 124 " --> pdb=" O LEU E 144 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 124 through 125 removed outlier: 3.573A pdb=" N TRP E 124 " --> pdb=" O LEU E 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 208 through 210 removed outlier: 6.426A pdb=" N ALA E 151 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS E 181 " --> pdb=" O ALA E 151 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N HIS E 153 " --> pdb=" O LYS E 181 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 358 through 359 removed outlier: 3.946A pdb=" N TYR E 381 " --> pdb=" O CYS E 358 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR E 378 " --> pdb=" O ALA E 401 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU E 403 " --> pdb=" O THR E 378 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 380 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ARG E 299 " --> pdb=" O VAL E 400 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ASN E 261 " --> pdb=" O ILE E 298 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 426 " --> pdb=" O CYS E 262 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLY E 425 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU E 452 " --> pdb=" O GLY E 425 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU E 427 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE E 449 " --> pdb=" O GLN F 500 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 539 through 541 removed outlier: 3.874A pdb=" N VAL E 655 " --> pdb=" O ALA E 664 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA E 664 " --> pdb=" O VAL E 655 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 545 through 547 removed outlier: 6.459A pdb=" N GLU E 650 " --> pdb=" O LYS E 631 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 608 through 609 Processing sheet with id=AE4, first strand: chain 'E' and resid 612 through 613 Processing sheet with id=AE5, first strand: chain 'F' and resid 3 through 4 removed outlier: 3.618A pdb=" N TRP F 32 " --> pdb=" O ILE F 22 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 6 through 8 Processing sheet with id=AE7, first strand: chain 'F' and resid 208 through 210 removed outlier: 6.218A pdb=" N ALA F 151 " --> pdb=" O ILE F 179 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS F 181 " --> pdb=" O ALA F 151 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS F 153 " --> pdb=" O LYS F 181 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 378 through 379 removed outlier: 6.754A pdb=" N THR F 378 " --> pdb=" O ALA F 401 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N LEU F 403 " --> pdb=" O THR F 378 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG F 299 " --> pdb=" O VAL F 400 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASN F 261 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLY F 425 " --> pdb=" O GLN F 450 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU F 452 " --> pdb=" O GLY F 425 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 427 " --> pdb=" O LEU F 452 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 540 through 541 Processing sheet with id=AF1, first strand: chain 'F' and resid 540 through 541 removed outlier: 6.459A pdb=" N GLU F 650 " --> pdb=" O LYS F 631 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL F 655 " --> pdb=" O ALA F 664 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ALA F 664 " --> pdb=" O VAL F 655 " (cutoff:3.500A) 1172 hydrogen bonds defined for protein. 3240 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: 6.44 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9294 1.33 - 1.46: 6728 1.46 - 1.58: 15286 1.58 - 1.71: 18 1.71 - 1.83: 252 Bond restraints: 31578 Sorted by residual: bond pdb=" CA VAL B 648 " pdb=" CB VAL B 648 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.05e-02 9.07e+03 3.14e+00 bond pdb=" N THR D 634 " pdb=" CA THR D 634 " ideal model delta sigma weight residual 1.461 1.481 -0.020 1.38e-02 5.25e+03 2.18e+00 bond pdb=" CB ASN F 158 " pdb=" CG ASN F 158 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.18e+00 bond pdb=" N THR C 634 " pdb=" CA THR C 634 " ideal model delta sigma weight residual 1.461 1.480 -0.019 1.38e-02 5.25e+03 1.94e+00 bond pdb=" CA VAL C 648 " pdb=" CB VAL C 648 " ideal model delta sigma weight residual 1.527 1.544 -0.017 1.31e-02 5.83e+03 1.75e+00 ... (remaining 31573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 41419 2.02 - 4.04: 1303 4.04 - 6.07: 138 6.07 - 8.09: 46 8.09 - 10.11: 12 Bond angle restraints: 42918 Sorted by residual: angle pdb=" C ASN B 606 " pdb=" N TYR B 607 " pdb=" CA TYR B 607 " ideal model delta sigma weight residual 121.54 128.62 -7.08 1.91e+00 2.74e-01 1.38e+01 angle pdb=" C ASN E 606 " pdb=" N TYR E 607 " pdb=" CA TYR E 607 " ideal model delta sigma weight residual 121.54 128.51 -6.97 1.91e+00 2.74e-01 1.33e+01 angle pdb=" C ASN D 606 " pdb=" N TYR D 607 " pdb=" CA TYR D 607 " ideal model delta sigma weight residual 121.54 128.45 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" C ASN F 606 " pdb=" N TYR F 607 " pdb=" CA TYR F 607 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C ASN C 606 " pdb=" N TYR C 607 " pdb=" CA TYR C 607 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 ... (remaining 42913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 18654 33.68 - 67.35: 172 67.35 - 101.03: 14 101.03 - 134.70: 1 134.70 - 168.38: 5 Dihedral angle restraints: 18846 sinusoidal: 7326 harmonic: 11520 Sorted by residual: dihedral pdb=" CA ASP E 522 " pdb=" C ASP E 522 " pdb=" N ARG E 523 " pdb=" CA ARG E 523 " ideal model delta harmonic sigma weight residual 180.00 155.48 24.52 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASP C 522 " pdb=" C ASP C 522 " pdb=" N ARG C 523 " pdb=" CA ARG C 523 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP A 522 " pdb=" C ASP A 522 " pdb=" N ARG A 523 " pdb=" CA ARG A 523 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 18843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3041 0.042 - 0.083: 1294 0.083 - 0.125: 471 0.125 - 0.167: 69 0.167 - 0.209: 9 Chirality restraints: 4884 Sorted by residual: chirality pdb=" CA TYR C 607 " pdb=" N TYR C 607 " pdb=" C TYR C 607 " pdb=" CB TYR C 607 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA TYR D 607 " pdb=" N TYR D 607 " pdb=" C TYR D 607 " pdb=" CB TYR D 607 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.05e+00 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 1.01e+00 ... (remaining 4881 not shown) Planarity restraints: 5598 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 124 " 0.019 2.00e-02 2.50e+03 1.75e-02 7.64e+00 pdb=" CG TRP B 124 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 124 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP B 124 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 124 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 124 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 124 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 124 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 124 " 0.019 2.00e-02 2.50e+03 1.60e-02 6.38e+00 pdb=" CG TRP F 124 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP F 124 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP F 124 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 124 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 124 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 124 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" CG TRP D 124 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP D 124 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP D 124 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 124 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 124 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 124 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 124 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 124 " 0.003 2.00e-02 2.50e+03 ... (remaining 5595 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 9248 2.82 - 3.34: 27258 3.34 - 3.86: 53030 3.86 - 4.38: 61445 4.38 - 4.90: 108476 Nonbonded interactions: 259457 Sorted by model distance: nonbonded pdb=" OG1 THR D 270 " pdb=" OD1 ASP D 272 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR F 270 " pdb=" OD1 ASP F 272 " model vdw 2.304 3.040 nonbonded pdb=" OG1 THR B 270 " pdb=" OD1 ASP B 272 " model vdw 2.312 3.040 nonbonded pdb=" OG1 THR A 270 " pdb=" OD1 ASP A 272 " model vdw 2.314 3.040 nonbonded pdb=" OG SER E 36 " pdb=" O SER E 214 " model vdw 2.318 3.040 ... (remaining 259452 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: 6.370 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.300 Find NCS groups from input model: 0.650 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.005 0.049 31578 Z= 0.223 Angle : 0.831 10.110 42918 Z= 0.443 Chirality : 0.051 0.209 4884 Planarity : 0.007 0.062 5598 Dihedral : 10.759 168.380 11442 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.06 % Allowed : 3.28 % Favored : 96.66 % 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: -4.47 (0.10), residues: 4056 helix: -3.10 (0.09), residues: 1368 sheet: -3.36 (0.16), residues: 654 loop : -2.67 (0.11), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 361 TYR 0.025 0.003 TYR C 607 PHE 0.023 0.003 PHE E 595 TRP 0.047 0.003 TRP B 124 HIS 0.015 0.002 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00524 (31578) covalent geometry : angle 0.83127 (42918) hydrogen bonds : bond 0.18107 ( 1163) hydrogen bonds : angle 8.90130 ( 3240) *********************** 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 697 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 695 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.8190 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 59 MET cc_start: 0.8504 (mtt) cc_final: 0.8277 (mtp) REVERT: B 217 ASP cc_start: 0.7800 (t0) cc_final: 0.7597 (t0) REVERT: B 333 LYS cc_start: 0.7837 (mttt) cc_final: 0.7353 (mttm) REVERT: B 532 GLU cc_start: 0.8148 (mp0) cc_final: 0.7890 (mp0) REVERT: B 611 SER cc_start: 0.7599 (t) cc_final: 0.7342 (p) REVERT: B 644 LYS cc_start: 0.8607 (mptm) cc_final: 0.8292 (mtpp) REVERT: C 242 VAL cc_start: 0.8801 (m) cc_final: 0.8547 (p) REVERT: C 417 CYS cc_start: 0.7979 (m) cc_final: 0.7637 (m) REVERT: C 532 GLU cc_start: 0.8135 (mp0) cc_final: 0.7735 (mp0) REVERT: D 164 MET cc_start: 0.9252 (tmt) cc_final: 0.8457 (tmt) REVERT: D 217 ASP cc_start: 0.7120 (t0) cc_final: 0.6858 (t0) REVERT: D 333 LYS cc_start: 0.7575 (mttt) cc_final: 0.7207 (mttm) REVERT: D 394 THR cc_start: 0.8672 (m) cc_final: 0.8247 (p) REVERT: D 505 MET cc_start: 0.8363 (tpp) cc_final: 0.8023 (mmt) REVERT: E 413 LEU cc_start: 0.8326 (mm) cc_final: 0.7718 (mp) REVERT: E 417 CYS cc_start: 0.8195 (m) cc_final: 0.7944 (m) REVERT: E 505 MET cc_start: 0.8072 (tpp) cc_final: 0.7772 (mmt) REVERT: F 7 PHE cc_start: 0.8785 (t80) cc_final: 0.8560 (t80) REVERT: F 333 LYS cc_start: 0.7705 (mttt) cc_final: 0.7243 (mttm) REVERT: F 532 GLU cc_start: 0.8259 (mp0) cc_final: 0.8050 (mp0) REVERT: F 611 SER cc_start: 0.7740 (t) cc_final: 0.7419 (p) REVERT: F 644 LYS cc_start: 0.8442 (mptm) cc_final: 0.8210 (mtpp) outliers start: 2 outliers final: 0 residues processed: 696 average time/residue: 0.2240 time to fit residues: 233.4433 Evaluate side-chains 325 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 HIS B 158 ASN B 351 ASN B 409 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 HIS ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN D 463 HIS ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 HIS E 500 GLN F 158 ASN F 342 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 409 GLN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.093882 restraints weight = 42538.623| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.53 r_work: 0.2942 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31578 Z= 0.171 Angle : 0.594 9.500 42918 Z= 0.307 Chirality : 0.043 0.154 4884 Planarity : 0.006 0.049 5598 Dihedral : 7.796 172.444 4392 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.76 % Allowed : 7.81 % Favored : 90.42 % 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: -3.14 (0.12), residues: 4056 helix: -1.44 (0.13), residues: 1386 sheet: -3.06 (0.16), residues: 708 loop : -2.09 (0.12), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 523 TYR 0.025 0.002 TYR C 607 PHE 0.033 0.002 PHE E 595 TRP 0.022 0.002 TRP A 124 HIS 0.007 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00403 (31578) covalent geometry : angle 0.59413 (42918) hydrogen bonds : bond 0.03655 ( 1163) hydrogen bonds : angle 5.83815 ( 3240) *********************** 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 419 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 363 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 311 VAL cc_start: 0.9061 (t) cc_final: 0.8830 (t) REVERT: B 217 ASP cc_start: 0.7974 (t0) cc_final: 0.7706 (t0) REVERT: B 268 ASP cc_start: 0.7534 (p0) cc_final: 0.7219 (p0) REVERT: B 333 LYS cc_start: 0.7784 (mttt) cc_final: 0.7508 (mttm) REVERT: C 387 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 505 MET cc_start: 0.9033 (tpp) cc_final: 0.8780 (tpp) REVERT: D 41 MET cc_start: 0.8922 (mmt) cc_final: 0.8394 (mmt) REVERT: D 164 MET cc_start: 0.9219 (tmt) cc_final: 0.8677 (tmt) REVERT: D 217 ASP cc_start: 0.7392 (t0) cc_final: 0.7101 (t0) REVERT: D 330 GLU cc_start: 0.7730 (tp30) cc_final: 0.7444 (tp30) REVERT: D 333 LYS cc_start: 0.7765 (mttt) cc_final: 0.7435 (mttm) REVERT: D 351 ASN cc_start: 0.8754 (m110) cc_final: 0.7880 (m-40) REVERT: D 505 MET cc_start: 0.8965 (tpp) cc_final: 0.8706 (mmt) REVERT: D 567 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8486 (tpt) REVERT: E 164 MET cc_start: 0.8923 (ttp) cc_final: 0.8716 (ttt) REVERT: E 413 LEU cc_start: 0.8463 (mm) cc_final: 0.7864 (mp) REVERT: E 417 CYS cc_start: 0.8377 (m) cc_final: 0.8154 (m) REVERT: E 463 HIS cc_start: 0.8794 (t70) cc_final: 0.8280 (t70) REVERT: E 505 MET cc_start: 0.8656 (tpp) cc_final: 0.8408 (mmt) REVERT: F 333 LYS cc_start: 0.7626 (mttt) cc_final: 0.7305 (mttm) REVERT: F 351 ASN cc_start: 0.8759 (m-40) cc_final: 0.8381 (m-40) outliers start: 56 outliers final: 28 residues processed: 401 average time/residue: 0.2022 time to fit residues: 126.6118 Evaluate side-chains 304 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 567 MET Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 616 GLU Chi-restraints excluded: chain E residue 623 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 160 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 348 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 387 optimal weight: 2.9990 chunk 391 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN A 433 GLN A 606 ASN B 409 GLN B 500 GLN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 554 ASN B 659 HIS ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 HIS ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN ** C 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 191 GLN D 261 ASN D 409 GLN D 554 ASN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 659 HIS ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.086797 restraints weight = 43232.495| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.69 r_work: 0.2816 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 31578 Z= 0.292 Angle : 0.660 8.370 42918 Z= 0.336 Chirality : 0.046 0.182 4884 Planarity : 0.005 0.047 5598 Dihedral : 7.857 178.598 4392 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.36 % Allowed : 9.96 % Favored : 87.68 % 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: -2.58 (0.12), residues: 4056 helix: -0.86 (0.13), residues: 1428 sheet: -2.84 (0.17), residues: 714 loop : -1.83 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 523 TYR 0.027 0.003 TYR C 607 PHE 0.028 0.002 PHE F 595 TRP 0.022 0.002 TRP E 124 HIS 0.007 0.001 HIS F 463 Details of bonding type rmsd covalent geometry : bond 0.00695 (31578) covalent geometry : angle 0.66029 (42918) hydrogen bonds : bond 0.03598 ( 1163) hydrogen bonds : angle 5.55643 ( 3240) *********************** 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 355 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 280 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.9075 (m-80) cc_final: 0.8825 (m-80) REVERT: A 243 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8060 (tm-30) REVERT: A 285 ARG cc_start: 0.8441 (tmm-80) cc_final: 0.8192 (ttp-170) REVERT: A 311 VAL cc_start: 0.9116 (t) cc_final: 0.8913 (t) REVERT: B 7 PHE cc_start: 0.8898 (t80) cc_final: 0.8681 (t80) REVERT: B 110 TYR cc_start: 0.9123 (m-80) cc_final: 0.8898 (m-80) REVERT: B 158 ASN cc_start: 0.8553 (m110) cc_final: 0.8332 (m-40) REVERT: B 217 ASP cc_start: 0.8023 (t0) cc_final: 0.7718 (t0) REVERT: B 333 LYS cc_start: 0.7762 (mttt) cc_final: 0.7494 (mttm) REVERT: C 387 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8347 (mt-10) REVERT: D 164 MET cc_start: 0.9312 (tmt) cc_final: 0.8748 (tmt) REVERT: D 217 ASP cc_start: 0.7660 (t0) cc_final: 0.7318 (t0) REVERT: D 330 GLU cc_start: 0.7710 (tp30) cc_final: 0.7410 (tp30) REVERT: D 333 LYS cc_start: 0.7799 (mttt) cc_final: 0.7404 (mttm) REVERT: E 413 LEU cc_start: 0.8572 (mm) cc_final: 0.8041 (mp) REVERT: E 417 CYS cc_start: 0.8359 (m) cc_final: 0.8117 (m) REVERT: E 505 MET cc_start: 0.8927 (tpp) cc_final: 0.8577 (mmt) REVERT: F 278 LEU cc_start: 0.8270 (pp) cc_final: 0.8069 (pp) REVERT: F 351 ASN cc_start: 0.8872 (m-40) cc_final: 0.8455 (m-40) outliers start: 75 outliers final: 39 residues processed: 335 average time/residue: 0.2030 time to fit residues: 105.7046 Evaluate side-chains 292 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 629 THR Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 281 ARG Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 606 ASN Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 616 GLU Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain F residue 616 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 289 optimal weight: 1.9990 chunk 212 optimal weight: 0.0470 chunk 43 optimal weight: 2.9990 chunk 258 optimal weight: 4.9990 chunk 321 optimal weight: 0.9990 chunk 394 optimal weight: 0.3980 chunk 180 optimal weight: 0.8980 chunk 341 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 352 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 ASN ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 HIS ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 347 GLN F 347 GLN F 351 ASN ** 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 = 0.3345 r_free = 0.3345 target = 0.115267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.092838 restraints weight = 42446.827| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.54 r_work: 0.2921 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31578 Z= 0.115 Angle : 0.529 7.568 42918 Z= 0.267 Chirality : 0.042 0.171 4884 Planarity : 0.004 0.037 5598 Dihedral : 7.456 173.384 4392 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.54 % Allowed : 11.47 % Favored : 86.99 % 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: -2.00 (0.13), residues: 4056 helix: -0.23 (0.14), residues: 1428 sheet: -2.54 (0.18), residues: 714 loop : -1.61 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 523 TYR 0.019 0.002 TYR C 607 PHE 0.027 0.001 PHE E 595 TRP 0.012 0.001 TRP E 124 HIS 0.006 0.001 HIS C 463 Details of bonding type rmsd covalent geometry : bond 0.00265 (31578) covalent geometry : angle 0.52854 (42918) hydrogen bonds : bond 0.02677 ( 1163) hydrogen bonds : angle 5.00666 ( 3240) *********************** 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 349 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 300 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8269 (m110) cc_final: 0.7900 (m-40) REVERT: A 243 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 311 VAL cc_start: 0.9122 (t) cc_final: 0.8875 (t) REVERT: A 547 MET cc_start: 0.8881 (mmt) cc_final: 0.8625 (mmt) REVERT: B 7 PHE cc_start: 0.8710 (t80) cc_final: 0.8466 (t80) REVERT: B 158 ASN cc_start: 0.8342 (m110) cc_final: 0.8031 (m-40) REVERT: B 217 ASP cc_start: 0.7806 (t0) cc_final: 0.7529 (t0) REVERT: B 333 LYS cc_start: 0.7738 (mttt) cc_final: 0.7484 (mttm) REVERT: B 505 MET cc_start: 0.8887 (tpp) cc_final: 0.8647 (mmp) REVERT: C 417 CYS cc_start: 0.8189 (m) cc_final: 0.7966 (m) REVERT: C 463 HIS cc_start: 0.8747 (t-170) cc_final: 0.8544 (t-170) REVERT: D 158 ASN cc_start: 0.8550 (m-40) cc_final: 0.8260 (m-40) REVERT: D 164 MET cc_start: 0.9248 (tmt) cc_final: 0.8997 (tmt) REVERT: D 330 GLU cc_start: 0.7527 (tp30) cc_final: 0.7226 (tp30) REVERT: D 333 LYS cc_start: 0.7767 (mttt) cc_final: 0.7400 (mttm) REVERT: D 505 MET cc_start: 0.9153 (tpp) cc_final: 0.8743 (mmt) REVERT: D 547 MET cc_start: 0.8726 (mmt) cc_final: 0.8480 (mmt) REVERT: E 32 TRP cc_start: 0.8341 (m100) cc_final: 0.8039 (m100) REVERT: E 285 ARG cc_start: 0.8177 (tmm-80) cc_final: 0.7862 (ttp-170) REVERT: E 413 LEU cc_start: 0.8432 (mm) cc_final: 0.7849 (mp) REVERT: E 417 CYS cc_start: 0.8308 (m) cc_final: 0.8075 (m) REVERT: E 505 MET cc_start: 0.8760 (tpp) cc_final: 0.8404 (mmt) REVERT: F 7 PHE cc_start: 0.8739 (t80) cc_final: 0.8416 (t80) REVERT: F 41 MET cc_start: 0.9028 (mmt) cc_final: 0.8762 (mmt) REVERT: F 333 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7492 (mttm) REVERT: F 505 MET cc_start: 0.9114 (tpp) cc_final: 0.8719 (mmt) outliers start: 49 outliers final: 27 residues processed: 331 average time/residue: 0.2000 time to fit residues: 103.4708 Evaluate side-chains 281 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 96 optimal weight: 3.9990 chunk 344 optimal weight: 6.9990 chunk 310 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 226 optimal weight: 0.0970 chunk 225 optimal weight: 1.9990 chunk 398 optimal weight: 0.0060 chunk 285 optimal weight: 2.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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 659 HIS ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 GLN ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 409 GLN ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.098904 restraints weight = 43084.141| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.07 r_work: 0.3019 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31578 Z= 0.123 Angle : 0.523 7.933 42918 Z= 0.263 Chirality : 0.042 0.207 4884 Planarity : 0.004 0.038 5598 Dihedral : 7.287 172.419 4392 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.70 % Allowed : 12.26 % Favored : 86.04 % 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: -1.64 (0.13), residues: 4056 helix: 0.16 (0.14), residues: 1428 sheet: -2.39 (0.18), residues: 696 loop : -1.47 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 361 TYR 0.020 0.002 TYR C 607 PHE 0.024 0.001 PHE D 595 TRP 0.009 0.001 TRP D 651 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00289 (31578) covalent geometry : angle 0.52265 (42918) hydrogen bonds : bond 0.02633 ( 1163) hydrogen bonds : angle 4.83268 ( 3240) *********************** 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 332 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8478 (m110) cc_final: 0.8114 (m-40) REVERT: A 243 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 311 VAL cc_start: 0.9074 (t) cc_final: 0.8816 (t) REVERT: A 547 MET cc_start: 0.9009 (mmt) cc_final: 0.8785 (mmt) REVERT: B 7 PHE cc_start: 0.8661 (t80) cc_final: 0.8347 (t80) REVERT: B 158 ASN cc_start: 0.8556 (m110) cc_final: 0.8252 (m-40) REVERT: B 193 MET cc_start: 0.8921 (mtp) cc_final: 0.8617 (mtp) REVERT: B 217 ASP cc_start: 0.8007 (t0) cc_final: 0.7732 (t0) REVERT: B 333 LYS cc_start: 0.7938 (mttt) cc_final: 0.7457 (mttm) REVERT: B 505 MET cc_start: 0.8987 (tpp) cc_final: 0.8724 (mmp) REVERT: C 191 GLN cc_start: 0.8840 (tt0) cc_final: 0.8604 (tt0) REVERT: C 417 CYS cc_start: 0.8420 (m) cc_final: 0.8189 (m) REVERT: C 463 HIS cc_start: 0.8848 (t-170) cc_final: 0.8620 (t-170) REVERT: D 158 ASN cc_start: 0.8665 (m-40) cc_final: 0.8377 (m-40) REVERT: D 217 ASP cc_start: 0.7547 (p0) cc_final: 0.7310 (p0) REVERT: D 330 GLU cc_start: 0.7734 (tp30) cc_final: 0.7456 (tp30) REVERT: D 333 LYS cc_start: 0.7806 (mttt) cc_final: 0.7331 (mttm) REVERT: D 429 THR cc_start: 0.9586 (p) cc_final: 0.9313 (t) REVERT: D 505 MET cc_start: 0.9245 (tpp) cc_final: 0.8763 (mmt) REVERT: E 32 TRP cc_start: 0.8197 (m100) cc_final: 0.7893 (m100) REVERT: E 158 ASN cc_start: 0.8536 (m110) cc_final: 0.8291 (m-40) REVERT: E 193 MET cc_start: 0.8807 (ttm) cc_final: 0.8605 (mtt) REVERT: E 413 LEU cc_start: 0.8389 (mm) cc_final: 0.7825 (mp) REVERT: E 417 CYS cc_start: 0.8479 (m) cc_final: 0.8196 (m) REVERT: E 505 MET cc_start: 0.8887 (tpp) cc_final: 0.8485 (mmt) REVERT: E 610 GLU cc_start: 0.7877 (tp30) cc_final: 0.7534 (mm-30) REVERT: F 7 PHE cc_start: 0.8667 (t80) cc_final: 0.8298 (t80) REVERT: F 41 MET cc_start: 0.8979 (mmt) cc_final: 0.8722 (mmt) REVERT: F 121 ASP cc_start: 0.8535 (t0) cc_final: 0.8262 (t0) REVERT: F 333 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7289 (mttm) REVERT: F 505 MET cc_start: 0.9204 (tpp) cc_final: 0.8755 (mmt) outliers start: 54 outliers final: 36 residues processed: 322 average time/residue: 0.1925 time to fit residues: 99.4587 Evaluate side-chains 287 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 379 LEU Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 623 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 391 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 351 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.108760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.084761 restraints weight = 43363.162| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.69 r_work: 0.2782 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.056 31578 Z= 0.328 Angle : 0.671 8.324 42918 Z= 0.340 Chirality : 0.047 0.205 4884 Planarity : 0.005 0.059 5598 Dihedral : 7.746 178.793 4392 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.33 % Allowed : 12.57 % Favored : 85.10 % 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: -1.80 (0.13), residues: 4056 helix: 0.08 (0.14), residues: 1392 sheet: -2.55 (0.17), residues: 744 loop : -1.51 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 361 TYR 0.029 0.003 TYR A 607 PHE 0.024 0.002 PHE A 656 TRP 0.015 0.002 TRP C 124 HIS 0.005 0.001 HIS A 566 Details of bonding type rmsd covalent geometry : bond 0.00786 (31578) covalent geometry : angle 0.67144 (42918) hydrogen bonds : bond 0.03470 ( 1163) hydrogen bonds : angle 5.21681 ( 3240) *********************** 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 335 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 261 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 243 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 285 ARG cc_start: 0.8446 (tmm-80) cc_final: 0.8184 (ttp-170) REVERT: A 311 VAL cc_start: 0.9189 (t) cc_final: 0.8953 (t) REVERT: B 7 PHE cc_start: 0.8856 (t80) cc_final: 0.8604 (t80) REVERT: B 217 ASP cc_start: 0.7910 (t0) cc_final: 0.7663 (t0) REVERT: B 333 LYS cc_start: 0.7800 (mttt) cc_final: 0.7503 (mttm) REVERT: B 409 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7946 (tp40) REVERT: C 191 GLN cc_start: 0.8901 (tt0) cc_final: 0.8630 (tt0) REVERT: C 334 MET cc_start: 0.9021 (ttm) cc_final: 0.8814 (ttm) REVERT: D 158 ASN cc_start: 0.8672 (m-40) cc_final: 0.8436 (m110) REVERT: D 217 ASP cc_start: 0.7976 (p0) cc_final: 0.7772 (p0) REVERT: D 333 LYS cc_start: 0.7759 (mttt) cc_final: 0.7384 (mttm) REVERT: E 32 TRP cc_start: 0.8643 (m100) cc_final: 0.8224 (m100) REVERT: E 413 LEU cc_start: 0.8581 (mm) cc_final: 0.8045 (mp) REVERT: E 417 CYS cc_start: 0.8382 (m) cc_final: 0.8108 (m) REVERT: F 7 PHE cc_start: 0.8846 (t80) cc_final: 0.8542 (t80) REVERT: F 217 ASP cc_start: 0.8074 (t0) cc_final: 0.7871 (t0) REVERT: F 515 ARG cc_start: 0.7975 (tpp-160) cc_final: 0.7732 (tpt-90) outliers start: 74 outliers final: 52 residues processed: 319 average time/residue: 0.2012 time to fit residues: 100.3273 Evaluate side-chains 296 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 244 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 538 ASP Chi-restraints excluded: chain C residue 624 ILE Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 629 THR Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 514 VAL Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 611 SER Chi-restraints excluded: chain F residue 616 GLU Chi-restraints excluded: chain F residue 623 THR Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 319 optimal weight: 0.3980 chunk 353 optimal weight: 0.0770 chunk 315 optimal weight: 0.0670 chunk 205 optimal weight: 1.9990 chunk 392 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 213 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 119 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 260 optimal weight: 0.9980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 HIS ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 HIS ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.090312 restraints weight = 42295.200| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.17 r_work: 0.2866 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31578 Z= 0.104 Angle : 0.518 7.904 42918 Z= 0.262 Chirality : 0.041 0.198 4884 Planarity : 0.004 0.039 5598 Dihedral : 7.305 172.068 4392 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.67 % Allowed : 13.33 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.37 (0.13), residues: 4056 helix: 0.51 (0.15), residues: 1392 sheet: -2.28 (0.18), residues: 732 loop : -1.34 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 361 TYR 0.020 0.001 TYR E 607 PHE 0.024 0.001 PHE D 595 TRP 0.008 0.001 TRP C 651 HIS 0.006 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00239 (31578) covalent geometry : angle 0.51821 (42918) hydrogen bonds : bond 0.02538 ( 1163) hydrogen bonds : angle 4.75682 ( 3240) *********************** 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 339 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 0.936 Fit side-chains revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8422 (m110) cc_final: 0.8192 (m-40) REVERT: A 311 VAL cc_start: 0.8954 (t) cc_final: 0.8715 (t) REVERT: A 515 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.7229 (mmm160) REVERT: A 547 MET cc_start: 0.9129 (mmt) cc_final: 0.8842 (mmt) REVERT: B 7 PHE cc_start: 0.8611 (t80) cc_final: 0.8240 (t80) REVERT: B 18 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8098 (tmt170) REVERT: B 193 MET cc_start: 0.8900 (mtp) cc_final: 0.8622 (mtp) REVERT: B 217 ASP cc_start: 0.7844 (t0) cc_final: 0.7518 (t0) REVERT: B 333 LYS cc_start: 0.7886 (mttt) cc_final: 0.7336 (mttm) REVERT: B 351 ASN cc_start: 0.8821 (m110) cc_final: 0.8554 (m-40) REVERT: B 505 MET cc_start: 0.8944 (tpp) cc_final: 0.8616 (mmp) REVERT: B 515 ARG cc_start: 0.7755 (tpp-160) cc_final: 0.7393 (tpt-90) REVERT: D 158 ASN cc_start: 0.8573 (m-40) cc_final: 0.8300 (m-40) REVERT: D 330 GLU cc_start: 0.7827 (tp30) cc_final: 0.7491 (tp30) REVERT: D 333 LYS cc_start: 0.7545 (mttt) cc_final: 0.7022 (mttm) REVERT: D 351 ASN cc_start: 0.8643 (m110) cc_final: 0.7893 (m-40) REVERT: D 429 THR cc_start: 0.9629 (p) cc_final: 0.9260 (t) REVERT: D 505 MET cc_start: 0.9287 (tpp) cc_final: 0.8735 (mmt) REVERT: D 679 PHE cc_start: 0.5750 (OUTLIER) cc_final: 0.5042 (m-10) REVERT: E 32 TRP cc_start: 0.8188 (m100) cc_final: 0.7863 (m100) REVERT: E 413 LEU cc_start: 0.8179 (mm) cc_final: 0.7775 (mp) REVERT: E 417 CYS cc_start: 0.8598 (m) cc_final: 0.8302 (m) REVERT: E 523 ARG cc_start: 0.8178 (ttp-110) cc_final: 0.7939 (ttp80) REVERT: F 7 PHE cc_start: 0.8532 (t80) cc_final: 0.8097 (t80) REVERT: F 121 ASP cc_start: 0.8495 (t0) cc_final: 0.8149 (t0) REVERT: F 505 MET cc_start: 0.9089 (tpp) cc_final: 0.8569 (mmt) outliers start: 53 outliers final: 36 residues processed: 324 average time/residue: 0.1957 time to fit residues: 100.2044 Evaluate side-chains 294 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 629 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 629 THR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 490 VAL Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 17 optimal weight: 0.0870 chunk 276 optimal weight: 4.9990 chunk 216 optimal weight: 0.6980 chunk 52 optimal weight: 0.0970 chunk 164 optimal weight: 0.0060 chunk 239 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 99 optimal weight: 0.0770 chunk 316 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 overall best weight: 0.1730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS F 392 HIS ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093422 restraints weight = 42263.588| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.19 r_work: 0.2940 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31578 Z= 0.094 Angle : 0.503 7.243 42918 Z= 0.254 Chirality : 0.041 0.221 4884 Planarity : 0.004 0.054 5598 Dihedral : 7.022 167.162 4392 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.13 % Allowed : 14.05 % Favored : 84.81 % 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: -1.04 (0.13), residues: 4056 helix: 0.82 (0.15), residues: 1392 sheet: -2.17 (0.19), residues: 696 loop : -1.19 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 523 TYR 0.019 0.001 TYR A 607 PHE 0.025 0.001 PHE D 595 TRP 0.009 0.001 TRP D 651 HIS 0.009 0.000 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00214 (31578) covalent geometry : angle 0.50322 (42918) hydrogen bonds : bond 0.02361 ( 1163) hydrogen bonds : angle 4.55455 ( 3240) *********************** 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 322 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 286 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8665 (mtp) cc_final: 0.8370 (mtp) REVERT: A 311 VAL cc_start: 0.9048 (t) cc_final: 0.8815 (t) REVERT: A 429 THR cc_start: 0.9306 (p) cc_final: 0.9082 (t) REVERT: A 547 MET cc_start: 0.9113 (mmt) cc_final: 0.8799 (mmt) REVERT: B 7 PHE cc_start: 0.8591 (t80) cc_final: 0.8230 (t80) REVERT: B 18 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7973 (tmt170) REVERT: B 121 ASP cc_start: 0.8715 (t0) cc_final: 0.8485 (t0) REVERT: B 217 ASP cc_start: 0.7829 (t0) cc_final: 0.7522 (t0) REVERT: B 333 LYS cc_start: 0.7955 (mttt) cc_final: 0.7422 (mttm) REVERT: B 351 ASN cc_start: 0.8795 (m110) cc_final: 0.8521 (m-40) REVERT: B 505 MET cc_start: 0.8928 (tpp) cc_final: 0.8632 (mmp) REVERT: D 7 PHE cc_start: 0.8446 (t80) cc_final: 0.8108 (t80) REVERT: D 158 ASN cc_start: 0.8554 (m-40) cc_final: 0.8262 (m-40) REVERT: D 330 GLU cc_start: 0.7796 (tp30) cc_final: 0.7447 (tp30) REVERT: D 333 LYS cc_start: 0.7587 (mttt) cc_final: 0.7116 (mttm) REVERT: D 351 ASN cc_start: 0.8626 (m110) cc_final: 0.7907 (m-40) REVERT: D 429 THR cc_start: 0.9590 (p) cc_final: 0.9307 (t) REVERT: D 505 MET cc_start: 0.9313 (tpp) cc_final: 0.8812 (mmt) REVERT: D 679 PHE cc_start: 0.5785 (OUTLIER) cc_final: 0.4965 (m-10) REVERT: E 158 ASN cc_start: 0.8524 (m110) cc_final: 0.8208 (m-40) REVERT: E 413 LEU cc_start: 0.8134 (mm) cc_final: 0.7673 (mp) REVERT: E 417 CYS cc_start: 0.8609 (m) cc_final: 0.8296 (m) REVERT: E 610 GLU cc_start: 0.7900 (tp30) cc_final: 0.7485 (mm-30) REVERT: F 7 PHE cc_start: 0.8490 (t80) cc_final: 0.8086 (t80) REVERT: F 217 ASP cc_start: 0.7899 (t0) cc_final: 0.7678 (t0) REVERT: F 333 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7051 (mttm) REVERT: F 394 THR cc_start: 0.8831 (m) cc_final: 0.8264 (p) REVERT: F 505 MET cc_start: 0.9071 (tpp) cc_final: 0.8562 (mmt) outliers start: 36 outliers final: 21 residues processed: 315 average time/residue: 0.1880 time to fit residues: 96.2996 Evaluate side-chains 278 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 255 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 417 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 2 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 359 optimal weight: 0.0030 chunk 151 optimal weight: 0.0870 chunk 3 optimal weight: 6.9990 chunk 216 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 336 optimal weight: 9.9990 overall best weight: 0.6170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 GLN ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.091798 restraints weight = 42402.317| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.19 r_work: 0.2927 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31578 Z= 0.119 Angle : 0.521 7.558 42918 Z= 0.262 Chirality : 0.042 0.212 4884 Planarity : 0.004 0.042 5598 Dihedral : 6.923 164.799 4392 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.39 % Allowed : 13.99 % Favored : 84.63 % 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: -0.95 (0.13), residues: 4056 helix: 0.92 (0.14), residues: 1392 sheet: -2.13 (0.18), residues: 696 loop : -1.15 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 523 TYR 0.024 0.002 TYR F 585 PHE 0.024 0.001 PHE D 595 TRP 0.024 0.001 TRP D 162 HIS 0.009 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00283 (31578) covalent geometry : angle 0.52135 (42918) hydrogen bonds : bond 0.02449 ( 1163) hydrogen bonds : angle 4.59138 ( 3240) *********************** 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 307 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: A 193 MET cc_start: 0.8707 (mtp) cc_final: 0.8435 (mtp) REVERT: A 311 VAL cc_start: 0.9065 (t) cc_final: 0.8835 (t) REVERT: B 7 PHE cc_start: 0.8618 (t80) cc_final: 0.8246 (t80) REVERT: B 121 ASP cc_start: 0.8686 (t0) cc_final: 0.8474 (t0) REVERT: B 217 ASP cc_start: 0.7810 (t0) cc_final: 0.7489 (t0) REVERT: B 256 GLU cc_start: 0.7725 (tt0) cc_final: 0.7423 (tm-30) REVERT: B 333 LYS cc_start: 0.7881 (mttt) cc_final: 0.7300 (mttm) REVERT: B 515 ARG cc_start: 0.7561 (tpp-160) cc_final: 0.7304 (tpt-90) REVERT: D 158 ASN cc_start: 0.8605 (m-40) cc_final: 0.8302 (m-40) REVERT: D 193 MET cc_start: 0.8360 (mtt) cc_final: 0.8144 (mtp) REVERT: D 321 LYS cc_start: 0.8602 (mttp) cc_final: 0.8291 (mmtm) REVERT: D 330 GLU cc_start: 0.7794 (tp30) cc_final: 0.7420 (tp30) REVERT: D 333 LYS cc_start: 0.7518 (mttt) cc_final: 0.7099 (mttm) REVERT: D 351 ASN cc_start: 0.8668 (m110) cc_final: 0.7929 (m-40) REVERT: D 429 THR cc_start: 0.9581 (p) cc_final: 0.9325 (t) REVERT: D 679 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.5013 (m-10) REVERT: E 158 ASN cc_start: 0.8540 (m110) cc_final: 0.8249 (m-40) REVERT: E 285 ARG cc_start: 0.8208 (tmm-80) cc_final: 0.7900 (tmm-80) REVERT: E 413 LEU cc_start: 0.8204 (mm) cc_final: 0.7691 (mp) REVERT: E 417 CYS cc_start: 0.8627 (m) cc_final: 0.8297 (m) REVERT: E 607 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8816 (p90) REVERT: E 610 GLU cc_start: 0.7884 (tp30) cc_final: 0.7406 (mm-30) REVERT: F 7 PHE cc_start: 0.8518 (t80) cc_final: 0.8129 (t80) REVERT: F 217 ASP cc_start: 0.7797 (t0) cc_final: 0.7546 (t0) REVERT: F 505 MET cc_start: 0.9070 (tpp) cc_final: 0.8558 (mmt) REVERT: F 515 ARG cc_start: 0.7444 (tpp-160) cc_final: 0.7172 (tpt-90) outliers start: 44 outliers final: 33 residues processed: 297 average time/residue: 0.1941 time to fit residues: 91.3181 Evaluate side-chains 285 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 200 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 269 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 319 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 307 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.089322 restraints weight = 42493.994| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.17 r_work: 0.2912 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31578 Z= 0.137 Angle : 0.532 7.396 42918 Z= 0.267 Chirality : 0.042 0.212 4884 Planarity : 0.004 0.048 5598 Dihedral : 6.886 161.955 4392 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.29 % Allowed : 14.18 % Favored : 84.53 % 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: -0.91 (0.13), residues: 4056 helix: 0.97 (0.14), residues: 1392 sheet: -2.13 (0.18), residues: 696 loop : -1.13 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 523 TYR 0.030 0.002 TYR F 585 PHE 0.023 0.001 PHE D 595 TRP 0.022 0.001 TRP C 97 HIS 0.010 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00326 (31578) covalent geometry : angle 0.53166 (42918) hydrogen bonds : bond 0.02539 ( 1163) hydrogen bonds : angle 4.63046 ( 3240) ********************** 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 298 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 257 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 158 ASN cc_start: 0.8486 (m110) cc_final: 0.8247 (m-40) REVERT: A 193 MET cc_start: 0.8711 (mtp) cc_final: 0.8460 (mtp) REVERT: A 311 VAL cc_start: 0.9072 (t) cc_final: 0.8841 (t) REVERT: A 547 MET cc_start: 0.9072 (mmt) cc_final: 0.8825 (mmt) REVERT: B 7 PHE cc_start: 0.8635 (t80) cc_final: 0.8293 (t80) REVERT: B 217 ASP cc_start: 0.7795 (t0) cc_final: 0.7467 (t0) REVERT: B 256 GLU cc_start: 0.7702 (tt0) cc_final: 0.7459 (tm-30) REVERT: B 333 LYS cc_start: 0.7842 (mttt) cc_final: 0.7600 (mmmt) REVERT: B 515 ARG cc_start: 0.7639 (tpp-160) cc_final: 0.7355 (tpt-90) REVERT: D 158 ASN cc_start: 0.8662 (m-40) cc_final: 0.8379 (m-40) REVERT: D 321 LYS cc_start: 0.8584 (mttp) cc_final: 0.8254 (mmtm) REVERT: D 333 LYS cc_start: 0.7564 (mttt) cc_final: 0.7117 (mttm) REVERT: D 429 THR cc_start: 0.9580 (p) cc_final: 0.9327 (t) REVERT: D 505 MET cc_start: 0.9400 (tpp) cc_final: 0.8804 (mmt) REVERT: D 679 PHE cc_start: 0.5910 (OUTLIER) cc_final: 0.5167 (m-10) REVERT: E 193 MET cc_start: 0.8754 (ttm) cc_final: 0.8524 (mtt) REVERT: E 413 LEU cc_start: 0.8257 (mm) cc_final: 0.7752 (mp) REVERT: E 417 CYS cc_start: 0.8667 (m) cc_final: 0.8332 (m) REVERT: E 607 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8849 (p90) REVERT: E 610 GLU cc_start: 0.7905 (tp30) cc_final: 0.7438 (mm-30) REVERT: F 7 PHE cc_start: 0.8535 (t80) cc_final: 0.8134 (t80) REVERT: F 217 ASP cc_start: 0.7811 (t0) cc_final: 0.7557 (t0) REVERT: F 333 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7138 (mttm) REVERT: F 409 GLN cc_start: 0.8260 (tp-100) cc_final: 0.8047 (tp-100) REVERT: F 410 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7777 (tpp-160) REVERT: F 505 MET cc_start: 0.9088 (tpp) cc_final: 0.8565 (mmt) REVERT: F 515 ARG cc_start: 0.7569 (tpp-160) cc_final: 0.7202 (tpt-90) outliers start: 41 outliers final: 35 residues processed: 287 average time/residue: 0.2000 time to fit residues: 90.3124 Evaluate side-chains 292 residues out of total 3174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 667 SER Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 667 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 667 SER Chi-restraints excluded: chain D residue 679 PHE Chi-restraints excluded: chain E residue 67 MET Chi-restraints excluded: chain E residue 164 MET Chi-restraints excluded: chain E residue 189 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 404 MET Chi-restraints excluded: chain E residue 549 GLU Chi-restraints excluded: chain E residue 596 VAL Chi-restraints excluded: chain E residue 607 TYR Chi-restraints excluded: chain E residue 648 VAL Chi-restraints excluded: chain F residue 49 ILE Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 417 CYS Chi-restraints excluded: chain F residue 629 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 171 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 394 optimal weight: 3.9990 chunk 297 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.088503 restraints weight = 42722.984| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.20 r_work: 0.2788 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 31578 Z= 0.184 Angle : 0.567 9.811 42918 Z= 0.285 Chirality : 0.043 0.206 4884 Planarity : 0.004 0.044 5598 Dihedral : 6.981 161.770 4392 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.48 % Allowed : 13.99 % Favored : 84.53 % 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: -0.96 (0.13), residues: 4056 helix: 0.92 (0.14), residues: 1392 sheet: -2.18 (0.18), residues: 714 loop : -1.12 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 523 TYR 0.026 0.002 TYR A 607 PHE 0.022 0.002 PHE D 595 TRP 0.023 0.001 TRP C 97 HIS 0.010 0.001 HIS A 463 Details of bonding type rmsd covalent geometry : bond 0.00442 (31578) covalent geometry : angle 0.56742 (42918) hydrogen bonds : bond 0.02765 ( 1163) hydrogen bonds : angle 4.74955 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6436.60 seconds wall clock time: 111 minutes 22.33 seconds (6682.33 seconds total)