Starting phenix.real_space_refine on Sun Jun 7 23:19:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21jv_67740/06_2026/21jv_67740.cif Found real_map, /net/cci-nas-00/data/ceres_data/21jv_67740/06_2026/21jv_67740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21jv_67740/06_2026/21jv_67740.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21jv_67740/06_2026/21jv_67740.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21jv_67740/06_2026/21jv_67740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21jv_67740/06_2026/21jv_67740.map" } resolution = 2.65 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= 0.005 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 16 5.49 5 S 240 5.16 5 C 26488 2.51 5 N 7096 2.21 5 O 10323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44163 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "B" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "C" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "D" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "E" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "F" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "G" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "H" Number of atoms: 5178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5178 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 49, 'TRANS': 612} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 298 Classifications: {'water': 298} Link IDs: {None: 297} Chain: "B" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 294 Classifications: {'water': 294} Link IDs: {None: 293} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 305 Classifications: {'water': 305} Link IDs: {None: 304} Chain: "D" Number of atoms: 298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 298 Classifications: {'water': 298} Link IDs: {None: 297} Chain: "E" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 281 Classifications: {'water': 281} Link IDs: {None: 280} Chain: "F" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 283 Classifications: {'water': 283} Link IDs: {None: 282} Chain: "G" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 280 Classifications: {'water': 280} Link IDs: {None: 279} Chain: "H" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 276 Classifications: {'water': 276} Link IDs: {None: 275} Time building chain proxies: 9.95, per 1000 atoms: 0.23 Number of scatterers: 44163 At special positions: 0 Unit cell: (148.963, 148.963, 137.441, 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 240 16.00 P 16 15.00 O 10323 8.00 N 7096 7.00 C 26488 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: 3.88 Conformation dependent library (CDL) restraints added in 1.8 seconds 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9776 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 80 sheets defined 36.9% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.544A pdb=" N TYR A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Proline residue: A 56 - end of helix removed outlier: 3.693A pdb=" N ARG A 60 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 105 through 111 removed outlier: 3.941A pdb=" N TYR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 129 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 158 through 169 removed outlier: 3.964A pdb=" N ASP A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.847A pdb=" N LEU A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 332 through 347 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.585A pdb=" N THR A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.785A pdb=" N THR A 371 " --> pdb=" O GLU A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 384 Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 469 removed outlier: 4.170A pdb=" N MET A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.565A pdb=" N GLN A 537 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'A' and resid 640 through 645 Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.547A pdb=" N THR A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 52 through 60 removed outlier: 3.545A pdb=" N TYR B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Proline residue: B 56 - end of helix removed outlier: 3.694A pdb=" N ARG B 60 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 105 through 111 removed outlier: 3.941A pdb=" N TYR B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 129 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 158 through 169 removed outlier: 3.962A pdb=" N ASP B 162 " --> pdb=" O PRO B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 271 through 280 removed outlier: 3.853A pdb=" N LEU B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 291 Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 332 through 347 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.582A pdb=" N THR B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.780A pdb=" N THR B 371 " --> pdb=" O GLU B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 384 Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 449 through 452 Processing helix chain 'B' and resid 453 through 469 Processing helix chain 'B' and resid 496 through 505 Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.541A pdb=" N GLN B 537 " --> pdb=" O TYR B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 562 Processing helix chain 'B' and resid 605 through 609 Processing helix chain 'B' and resid 617 through 636 Processing helix chain 'B' and resid 640 through 645 Processing helix chain 'B' and resid 654 through 659 removed outlier: 3.551A pdb=" N THR B 658 " --> pdb=" O THR B 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 27 Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.546A pdb=" N TYR C 55 " --> pdb=" O PRO C 52 " (cutoff:3.500A) Proline residue: C 56 - end of helix removed outlier: 3.696A pdb=" N ARG C 60 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 105 through 111 removed outlier: 3.941A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 129 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 158 through 169 removed outlier: 3.969A pdb=" N ASP C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 271 through 280 removed outlier: 3.851A pdb=" N LEU C 275 " --> pdb=" O ILE C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 291 Processing helix chain 'C' and resid 325 through 331 Processing helix chain 'C' and resid 332 through 347 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.582A pdb=" N THR C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.780A pdb=" N THR C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 384 Processing helix chain 'C' and resid 404 through 408 Processing helix chain 'C' and resid 449 through 452 Processing helix chain 'C' and resid 453 through 469 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 533 through 537 removed outlier: 3.547A pdb=" N GLN C 537 " --> pdb=" O TYR C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 562 Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 617 through 636 Processing helix chain 'C' and resid 640 through 645 Processing helix chain 'C' and resid 654 through 659 removed outlier: 3.551A pdb=" N THR C 658 " --> pdb=" O THR C 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.547A pdb=" N TYR D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 56 - end of helix removed outlier: 3.702A pdb=" N ARG D 60 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 105 through 111 removed outlier: 3.944A pdb=" N TYR D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 138 through 142 Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.953A pdb=" N ASP D 162 " --> pdb=" O PRO D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.848A pdb=" N LEU D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 291 Processing helix chain 'D' and resid 325 through 331 Processing helix chain 'D' and resid 332 through 347 Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.584A pdb=" N THR D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 removed outlier: 3.792A pdb=" N THR D 371 " --> pdb=" O GLU D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 384 Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 449 through 452 Processing helix chain 'D' and resid 453 through 469 Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 533 through 537 removed outlier: 3.502A pdb=" N GLN D 537 " --> pdb=" O TYR D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 562 Processing helix chain 'D' and resid 605 through 609 Processing helix chain 'D' and resid 617 through 636 Processing helix chain 'D' and resid 640 through 645 Processing helix chain 'D' and resid 654 through 659 removed outlier: 3.553A pdb=" N THR D 658 " --> pdb=" O THR D 654 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 27 Processing helix chain 'E' and resid 46 through 51 Processing helix chain 'E' and resid 52 through 60 removed outlier: 3.548A pdb=" N TYR E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Proline residue: E 56 - end of helix removed outlier: 3.700A pdb=" N ARG E 60 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 105 through 111 removed outlier: 3.949A pdb=" N TYR E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 129 Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.946A pdb=" N ASP E 162 " --> pdb=" O PRO E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 209 through 216 Processing helix chain 'E' and resid 271 through 280 removed outlier: 3.849A pdb=" N LEU E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 291 Processing helix chain 'E' and resid 325 through 330 Processing helix chain 'E' and resid 332 through 347 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.583A pdb=" N THR E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 removed outlier: 3.789A pdb=" N THR E 371 " --> pdb=" O GLU E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 384 Processing helix chain 'E' and resid 404 through 408 Processing helix chain 'E' and resid 449 through 452 Processing helix chain 'E' and resid 453 through 469 Processing helix chain 'E' and resid 496 through 505 Processing helix chain 'E' and resid 547 through 562 Processing helix chain 'E' and resid 605 through 609 Processing helix chain 'E' and resid 617 through 636 Processing helix chain 'E' and resid 640 through 645 Processing helix chain 'E' and resid 654 through 659 removed outlier: 3.548A pdb=" N THR E 658 " --> pdb=" O THR E 654 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 27 Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 52 through 60 removed outlier: 3.546A pdb=" N TYR F 55 " --> pdb=" O PRO F 52 " (cutoff:3.500A) Proline residue: F 56 - end of helix removed outlier: 3.697A pdb=" N ARG F 60 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 105 through 111 removed outlier: 3.940A pdb=" N TYR F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 158 through 169 removed outlier: 3.963A pdb=" N ASP F 162 " --> pdb=" O PRO F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 271 through 280 removed outlier: 3.853A pdb=" N LEU F 275 " --> pdb=" O ILE F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 291 Processing helix chain 'F' and resid 325 through 330 Processing helix chain 'F' and resid 332 through 347 Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.582A pdb=" N THR F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 371 removed outlier: 3.782A pdb=" N THR F 371 " --> pdb=" O GLU F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 384 Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 453 through 469 Processing helix chain 'F' and resid 496 through 505 Processing helix chain 'F' and resid 547 through 562 Processing helix chain 'F' and resid 605 through 609 Processing helix chain 'F' and resid 617 through 636 Processing helix chain 'F' and resid 640 through 645 Processing helix chain 'F' and resid 654 through 659 removed outlier: 3.546A pdb=" N THR F 658 " --> pdb=" O THR F 654 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 27 Processing helix chain 'G' and resid 46 through 51 Processing helix chain 'G' and resid 52 through 60 removed outlier: 3.545A pdb=" N TYR G 55 " --> pdb=" O PRO G 52 " (cutoff:3.500A) Proline residue: G 56 - end of helix removed outlier: 3.698A pdb=" N ARG G 60 " --> pdb=" O ARG G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 105 through 111 removed outlier: 3.949A pdb=" N TYR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 138 through 142 Processing helix chain 'G' and resid 158 through 169 removed outlier: 3.964A pdb=" N ASP G 162 " --> pdb=" O PRO G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 271 through 280 removed outlier: 3.849A pdb=" N LEU G 275 " --> pdb=" O ILE G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 291 Processing helix chain 'G' and resid 325 through 331 Processing helix chain 'G' and resid 332 through 347 Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.584A pdb=" N THR G 353 " --> pdb=" O PRO G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 371 removed outlier: 3.790A pdb=" N THR G 371 " --> pdb=" O GLU G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 384 Processing helix chain 'G' and resid 404 through 408 Processing helix chain 'G' and resid 449 through 452 Processing helix chain 'G' and resid 453 through 469 Processing helix chain 'G' and resid 496 through 505 Processing helix chain 'G' and resid 533 through 537 removed outlier: 3.545A pdb=" N GLN G 537 " --> pdb=" O TYR G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 562 Processing helix chain 'G' and resid 605 through 609 Processing helix chain 'G' and resid 617 through 636 Processing helix chain 'G' and resid 640 through 645 Processing helix chain 'G' and resid 654 through 659 removed outlier: 3.552A pdb=" N THR G 658 " --> pdb=" O THR G 654 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 27 Processing helix chain 'H' and resid 46 through 51 Processing helix chain 'H' and resid 52 through 60 removed outlier: 3.547A pdb=" N TYR H 55 " --> pdb=" O PRO H 52 " (cutoff:3.500A) Proline residue: H 56 - end of helix removed outlier: 3.700A pdb=" N ARG H 60 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 105 through 111 removed outlier: 3.946A pdb=" N TYR H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 138 through 142 Processing helix chain 'H' and resid 158 through 169 removed outlier: 3.958A pdb=" N ASP H 162 " --> pdb=" O PRO H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 209 Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 271 through 280 removed outlier: 3.851A pdb=" N LEU H 275 " --> pdb=" O ILE H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 291 Processing helix chain 'H' and resid 325 through 330 Processing helix chain 'H' and resid 332 through 347 Processing helix chain 'H' and resid 349 through 353 removed outlier: 3.583A pdb=" N THR H 353 " --> pdb=" O PRO H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 371 removed outlier: 3.783A pdb=" N THR H 371 " --> pdb=" O GLU H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 384 Processing helix chain 'H' and resid 404 through 408 Processing helix chain 'H' and resid 449 through 452 Processing helix chain 'H' and resid 453 through 469 Processing helix chain 'H' and resid 496 through 505 Processing helix chain 'H' and resid 533 through 537 Processing helix chain 'H' and resid 547 through 562 Processing helix chain 'H' and resid 605 through 609 Processing helix chain 'H' and resid 617 through 636 Processing helix chain 'H' and resid 640 through 645 Processing helix chain 'H' and resid 654 through 659 removed outlier: 3.555A pdb=" N THR H 658 " --> pdb=" O THR H 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.451A pdb=" N VAL A 34 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 222 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A 36 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE A 7 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN A 263 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 9 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE A 265 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 11 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA A 238 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N LYS A 262 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 10.344A pdb=" N VAL A 236 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ALA A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A 233 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 243 " --> pdb=" O ALA A 227 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA A 227 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 219 through 222 removed outlier: 6.451A pdb=" N VAL A 34 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 222 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU A 36 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE A 7 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLN A 263 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE A 9 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE A 265 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL A 11 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 66 through 69 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.385A pdb=" N LEU A 191 " --> pdb=" O TYR A 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AA6, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.386A pdb=" N ALA A 358 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 310 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N GLU A 476 " --> pdb=" O PRO A 315 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS A 317 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 186 through 189 removed outlier: 4.386A pdb=" N ALA A 358 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR A 310 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 194 through 195 Processing sheet with id=AA9, first strand: chain 'A' and resid 282 through 283 Processing sheet with id=AB1, first strand: chain 'A' and resid 428 through 430 Processing sheet with id=AB2, first strand: chain 'B' and resid 219 through 222 removed outlier: 6.473A pdb=" N VAL B 34 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 222 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 36 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE B 7 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN B 263 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE B 9 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE B 265 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 11 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA B 238 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N LYS B 262 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N VAL B 236 " --> pdb=" O LYS B 262 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA B 237 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 232 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY B 239 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N VAL B 230 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN B 241 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 219 through 222 removed outlier: 6.473A pdb=" N VAL B 34 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 222 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU B 36 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE B 7 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN B 263 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE B 9 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE B 265 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B 11 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 69 Processing sheet with id=AB5, first strand: chain 'B' and resid 100 through 101 removed outlier: 4.382A pdb=" N LEU B 191 " --> pdb=" O TYR B 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB7, first strand: chain 'B' and resid 186 through 189 removed outlier: 4.377A pdb=" N ALA B 358 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR B 310 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU B 476 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N HIS B 317 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 186 through 189 removed outlier: 4.377A pdb=" N ALA B 358 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR B 310 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 194 through 195 Processing sheet with id=AC1, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AC2, first strand: chain 'B' and resid 428 through 430 Processing sheet with id=AC3, first strand: chain 'C' and resid 219 through 222 removed outlier: 6.463A pdb=" N VAL C 34 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE C 222 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 36 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N PHE C 7 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN C 263 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE C 9 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE C 265 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL C 11 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA C 238 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N LYS C 262 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 10.354A pdb=" N VAL C 236 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU C 233 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL C 243 " --> pdb=" O ALA C 227 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA C 227 " --> pdb=" O VAL C 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 219 through 222 removed outlier: 6.463A pdb=" N VAL C 34 " --> pdb=" O TYR C 220 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE C 222 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU C 36 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N PHE C 7 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN C 263 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE C 9 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ILE C 265 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL C 11 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 66 through 69 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 101 removed outlier: 4.382A pdb=" N LEU C 191 " --> pdb=" O TYR C 101 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=AC8, first strand: chain 'C' and resid 186 through 189 removed outlier: 4.377A pdb=" N ALA C 358 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR C 310 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU C 476 " --> pdb=" O PRO C 315 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS C 317 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 186 through 189 removed outlier: 4.377A pdb=" N ALA C 358 " --> pdb=" O LEU C 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR C 310 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 194 through 195 Processing sheet with id=AD2, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AD3, first strand: chain 'C' and resid 428 through 430 Processing sheet with id=AD4, first strand: chain 'D' and resid 219 through 222 removed outlier: 6.457A pdb=" N VAL D 34 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 222 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU D 36 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE D 7 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN D 263 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE D 9 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE D 265 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL D 11 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA D 238 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N LYS D 262 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL D 236 " --> pdb=" O LYS D 262 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU D 233 " --> pdb=" O ALA D 237 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL D 243 " --> pdb=" O ALA D 227 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA D 227 " --> pdb=" O VAL D 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 219 through 222 removed outlier: 6.457A pdb=" N VAL D 34 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 222 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU D 36 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N PHE D 7 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLN D 263 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE D 9 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE D 265 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL D 11 " --> pdb=" O ILE D 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 66 through 69 Processing sheet with id=AD7, first strand: chain 'D' and resid 100 through 101 removed outlier: 4.387A pdb=" N LEU D 191 " --> pdb=" O TYR D 101 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=AD9, first strand: chain 'D' and resid 186 through 189 removed outlier: 4.377A pdb=" N ALA D 358 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D 310 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLU D 476 " --> pdb=" O PRO D 315 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N HIS D 317 " --> pdb=" O ALA D 474 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 186 through 189 removed outlier: 4.377A pdb=" N ALA D 358 " --> pdb=" O LEU D 397 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D 310 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 194 through 195 Processing sheet with id=AE3, first strand: chain 'D' and resid 282 through 283 Processing sheet with id=AE4, first strand: chain 'D' and resid 428 through 430 Processing sheet with id=AE5, first strand: chain 'E' and resid 219 through 222 removed outlier: 6.459A pdb=" N VAL E 34 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 222 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 36 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE E 7 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN E 263 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE E 9 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE E 265 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL E 11 " --> pdb=" O ILE E 265 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA E 238 " --> pdb=" O ALA E 260 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N LYS E 262 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 10.361A pdb=" N VAL E 236 " --> pdb=" O LYS E 262 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ALA E 237 " --> pdb=" O GLU E 233 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU E 233 " --> pdb=" O ALA E 237 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL E 243 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA E 227 " --> pdb=" O VAL E 243 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 219 through 222 removed outlier: 6.459A pdb=" N VAL E 34 " --> pdb=" O TYR E 220 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE E 222 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU E 36 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N PHE E 7 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLN E 263 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE E 9 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE E 265 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL E 11 " --> pdb=" O ILE E 265 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 66 through 69 Processing sheet with id=AE8, first strand: chain 'E' and resid 100 through 101 removed outlier: 4.383A pdb=" N LEU E 191 " --> pdb=" O TYR E 101 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 130 through 132 Processing sheet with id=AF1, first strand: chain 'E' and resid 186 through 189 removed outlier: 4.381A pdb=" N ALA E 358 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR E 310 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU E 476 " --> pdb=" O PRO E 315 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N HIS E 317 " --> pdb=" O ALA E 474 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 186 through 189 removed outlier: 4.381A pdb=" N ALA E 358 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR E 310 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 194 through 195 Processing sheet with id=AF4, first strand: chain 'E' and resid 282 through 283 Processing sheet with id=AF5, first strand: chain 'E' and resid 428 through 430 Processing sheet with id=AF6, first strand: chain 'F' and resid 219 through 222 removed outlier: 6.466A pdb=" N VAL F 34 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE F 222 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU F 36 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N PHE F 7 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN F 263 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE F 9 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE F 265 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL F 11 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ALA F 238 " --> pdb=" O ALA F 260 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N LYS F 262 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 10.330A pdb=" N VAL F 236 " --> pdb=" O LYS F 262 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA F 237 " --> pdb=" O GLU F 233 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLU F 233 " --> pdb=" O ALA F 237 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL F 243 " --> pdb=" O ALA F 227 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ALA F 227 " --> pdb=" O VAL F 243 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 219 through 222 removed outlier: 6.466A pdb=" N VAL F 34 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE F 222 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU F 36 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N PHE F 7 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN F 263 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE F 9 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE F 265 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL F 11 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 66 through 69 Processing sheet with id=AF9, first strand: chain 'F' and resid 100 through 101 removed outlier: 4.382A pdb=" N LEU F 191 " --> pdb=" O TYR F 101 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 130 through 132 Processing sheet with id=AG2, first strand: chain 'F' and resid 186 through 189 removed outlier: 4.391A pdb=" N ALA F 358 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR F 310 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU F 476 " --> pdb=" O PRO F 315 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N HIS F 317 " --> pdb=" O ALA F 474 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 186 through 189 removed outlier: 4.391A pdb=" N ALA F 358 " --> pdb=" O LEU F 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR F 310 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 194 through 195 Processing sheet with id=AG5, first strand: chain 'F' and resid 282 through 283 Processing sheet with id=AG6, first strand: chain 'F' and resid 428 through 430 Processing sheet with id=AG7, first strand: chain 'G' and resid 219 through 222 removed outlier: 6.465A pdb=" N VAL G 34 " --> pdb=" O TYR G 220 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE G 222 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU G 36 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE G 7 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN G 263 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE G 9 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE G 265 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL G 11 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ALA G 238 " --> pdb=" O ALA G 260 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N LYS G 262 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N VAL G 236 " --> pdb=" O LYS G 262 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA G 237 " --> pdb=" O GLU G 233 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU G 233 " --> pdb=" O ALA G 237 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL G 243 " --> pdb=" O ALA G 227 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA G 227 " --> pdb=" O VAL G 243 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 219 through 222 removed outlier: 6.465A pdb=" N VAL G 34 " --> pdb=" O TYR G 220 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ILE G 222 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU G 36 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N PHE G 7 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N GLN G 263 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE G 9 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE G 265 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL G 11 " --> pdb=" O ILE G 265 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 66 through 69 Processing sheet with id=AH1, first strand: chain 'G' and resid 100 through 101 removed outlier: 4.385A pdb=" N LEU G 191 " --> pdb=" O TYR G 101 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 130 through 132 Processing sheet with id=AH3, first strand: chain 'G' and resid 186 through 189 removed outlier: 4.382A pdb=" N ALA G 358 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR G 310 " --> pdb=" O LEU G 420 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU G 476 " --> pdb=" O PRO G 315 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N HIS G 317 " --> pdb=" O ALA G 474 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 186 through 189 removed outlier: 4.382A pdb=" N ALA G 358 " --> pdb=" O LEU G 397 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N TYR G 310 " --> pdb=" O LEU G 420 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 194 through 195 Processing sheet with id=AH6, first strand: chain 'G' and resid 282 through 283 Processing sheet with id=AH7, first strand: chain 'G' and resid 428 through 430 Processing sheet with id=AH8, first strand: chain 'H' and resid 219 through 222 removed outlier: 6.467A pdb=" N VAL H 34 " --> pdb=" O TYR H 220 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE H 222 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU H 36 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N PHE H 7 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN H 263 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE H 9 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE H 265 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL H 11 " --> pdb=" O ILE H 265 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N ALA H 238 " --> pdb=" O ALA H 260 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N LYS H 262 " --> pdb=" O VAL H 236 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N VAL H 236 " --> pdb=" O LYS H 262 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU H 233 " --> pdb=" O ALA H 237 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL H 243 " --> pdb=" O ALA H 227 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA H 227 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 219 through 222 removed outlier: 6.467A pdb=" N VAL H 34 " --> pdb=" O TYR H 220 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE H 222 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU H 36 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N PHE H 7 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN H 263 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ILE H 9 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE H 265 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL H 11 " --> pdb=" O ILE H 265 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 66 through 69 Processing sheet with id=AI2, first strand: chain 'H' and resid 100 through 101 removed outlier: 4.387A pdb=" N LEU H 191 " --> pdb=" O TYR H 101 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 130 through 132 Processing sheet with id=AI4, first strand: chain 'H' and resid 186 through 189 removed outlier: 4.374A pdb=" N ALA H 358 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR H 310 " --> pdb=" O LEU H 420 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU H 476 " --> pdb=" O PRO H 315 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N HIS H 317 " --> pdb=" O ALA H 474 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 186 through 189 removed outlier: 4.374A pdb=" N ALA H 358 " --> pdb=" O LEU H 397 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR H 310 " --> pdb=" O LEU H 420 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 194 through 195 Processing sheet with id=AI7, first strand: chain 'H' and resid 282 through 283 Processing sheet with id=AI8, first strand: chain 'H' and resid 428 through 430 1648 hydrogen bonds defined for protein. 4278 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.11 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13607 1.34 - 1.45: 6708 1.45 - 1.57: 22357 1.57 - 1.69: 32 1.69 - 1.81: 376 Bond restraints: 43080 Sorted by residual: bond pdb=" C4 FAD C 701 " pdb=" C4X FAD C 701 " ideal model delta sigma weight residual 1.481 1.405 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C4 FAD F 701 " pdb=" C4X FAD F 701 " ideal model delta sigma weight residual 1.481 1.405 0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C4 FAD H 701 " pdb=" C4X FAD H 701 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C4 FAD E 701 " pdb=" C4X FAD E 701 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C4 FAD A 701 " pdb=" C4X FAD A 701 " ideal model delta sigma weight residual 1.481 1.406 0.075 2.00e-02 2.50e+03 1.40e+01 ... (remaining 43075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 56785 1.16 - 2.32: 1299 2.32 - 3.49: 490 3.49 - 4.65: 64 4.65 - 5.81: 66 Bond angle restraints: 58704 Sorted by residual: angle pdb=" CA TYR H 395 " pdb=" CB TYR H 395 " pdb=" CG TYR H 395 " ideal model delta sigma weight residual 113.90 117.47 -3.57 1.80e+00 3.09e-01 3.92e+00 angle pdb=" CA TYR D 395 " pdb=" CB TYR D 395 " pdb=" CG TYR D 395 " ideal model delta sigma weight residual 113.90 117.46 -3.56 1.80e+00 3.09e-01 3.90e+00 angle pdb=" CA TYR E 395 " pdb=" CB TYR E 395 " pdb=" CG TYR E 395 " ideal model delta sigma weight residual 113.90 117.44 -3.54 1.80e+00 3.09e-01 3.88e+00 angle pdb=" CA TYR B 395 " pdb=" CB TYR B 395 " pdb=" CG TYR B 395 " ideal model delta sigma weight residual 113.90 117.44 -3.54 1.80e+00 3.09e-01 3.87e+00 angle pdb=" CA TYR A 395 " pdb=" CB TYR A 395 " pdb=" CG TYR A 395 " ideal model delta sigma weight residual 113.90 117.43 -3.53 1.80e+00 3.09e-01 3.84e+00 ... (remaining 58699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 24570 17.98 - 35.96: 936 35.96 - 53.94: 191 53.94 - 71.92: 31 71.92 - 89.91: 16 Dihedral angle restraints: 25744 sinusoidal: 10424 harmonic: 15320 Sorted by residual: dihedral pdb=" CA ASN B 616 " pdb=" C ASN B 616 " pdb=" N THR B 617 " pdb=" CA THR B 617 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ASN F 616 " pdb=" C ASN F 616 " pdb=" N THR F 617 " pdb=" CA THR F 617 " ideal model delta harmonic sigma weight residual 180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA ASN A 616 " pdb=" C ASN A 616 " pdb=" N THR A 617 " pdb=" CA THR A 617 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 25741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3918 0.036 - 0.071: 1482 0.071 - 0.107: 582 0.107 - 0.142: 194 0.142 - 0.178: 8 Chirality restraints: 6184 Sorted by residual: chirality pdb=" C3' FAD B 701 " pdb=" C2' FAD B 701 " pdb=" C4' FAD B 701 " pdb=" O3' FAD B 701 " both_signs ideal model delta sigma weight residual False -2.55 -2.37 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C3' FAD E 701 " pdb=" C2' FAD E 701 " pdb=" C4' FAD E 701 " pdb=" O3' FAD E 701 " both_signs ideal model delta sigma weight residual False -2.55 -2.37 -0.18 2.00e-01 2.50e+01 7.89e-01 chirality pdb=" C3' FAD G 701 " pdb=" C2' FAD G 701 " pdb=" C4' FAD G 701 " pdb=" O3' FAD G 701 " both_signs ideal model delta sigma weight residual False -2.55 -2.37 -0.18 2.00e-01 2.50e+01 7.89e-01 ... (remaining 6181 not shown) Planarity restraints: 7656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD G 701 " -0.298 2.00e-02 2.50e+03 1.97e-01 1.85e+03 pdb=" C10 FAD G 701 " -0.122 2.00e-02 2.50e+03 pdb=" C2 FAD G 701 " 0.207 2.00e-02 2.50e+03 pdb=" C4 FAD G 701 " 0.010 2.00e-02 2.50e+03 pdb=" C4X FAD G 701 " -0.152 2.00e-02 2.50e+03 pdb=" C5X FAD G 701 " -0.186 2.00e-02 2.50e+03 pdb=" C6 FAD G 701 " -0.075 2.00e-02 2.50e+03 pdb=" C7 FAD G 701 " 0.090 2.00e-02 2.50e+03 pdb=" C7M FAD G 701 " 0.215 2.00e-02 2.50e+03 pdb=" C8 FAD G 701 " 0.134 2.00e-02 2.50e+03 pdb=" C8M FAD G 701 " 0.303 2.00e-02 2.50e+03 pdb=" C9 FAD G 701 " 0.020 2.00e-02 2.50e+03 pdb=" C9A FAD G 701 " -0.145 2.00e-02 2.50e+03 pdb=" N1 FAD G 701 " 0.045 2.00e-02 2.50e+03 pdb=" N10 FAD G 701 " -0.271 2.00e-02 2.50e+03 pdb=" N3 FAD G 701 " 0.185 2.00e-02 2.50e+03 pdb=" N5 FAD G 701 " -0.321 2.00e-02 2.50e+03 pdb=" O2 FAD G 701 " 0.364 2.00e-02 2.50e+03 pdb=" O4 FAD G 701 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 701 " -0.297 2.00e-02 2.50e+03 1.97e-01 1.85e+03 pdb=" C10 FAD C 701 " -0.122 2.00e-02 2.50e+03 pdb=" C2 FAD C 701 " 0.207 2.00e-02 2.50e+03 pdb=" C4 FAD C 701 " 0.010 2.00e-02 2.50e+03 pdb=" C4X FAD C 701 " -0.152 2.00e-02 2.50e+03 pdb=" C5X FAD C 701 " -0.186 2.00e-02 2.50e+03 pdb=" C6 FAD C 701 " -0.075 2.00e-02 2.50e+03 pdb=" C7 FAD C 701 " 0.089 2.00e-02 2.50e+03 pdb=" C7M FAD C 701 " 0.215 2.00e-02 2.50e+03 pdb=" C8 FAD C 701 " 0.134 2.00e-02 2.50e+03 pdb=" C8M FAD C 701 " 0.303 2.00e-02 2.50e+03 pdb=" C9 FAD C 701 " 0.020 2.00e-02 2.50e+03 pdb=" C9A FAD C 701 " -0.144 2.00e-02 2.50e+03 pdb=" N1 FAD C 701 " 0.046 2.00e-02 2.50e+03 pdb=" N10 FAD C 701 " -0.271 2.00e-02 2.50e+03 pdb=" N3 FAD C 701 " 0.185 2.00e-02 2.50e+03 pdb=" N5 FAD C 701 " -0.321 2.00e-02 2.50e+03 pdb=" O2 FAD C 701 " 0.364 2.00e-02 2.50e+03 pdb=" O4 FAD C 701 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD B 701 " 0.297 2.00e-02 2.50e+03 1.97e-01 1.85e+03 pdb=" C10 FAD B 701 " 0.122 2.00e-02 2.50e+03 pdb=" C2 FAD B 701 " -0.207 2.00e-02 2.50e+03 pdb=" C4 FAD B 701 " -0.010 2.00e-02 2.50e+03 pdb=" C4X FAD B 701 " 0.152 2.00e-02 2.50e+03 pdb=" C5X FAD B 701 " 0.186 2.00e-02 2.50e+03 pdb=" C6 FAD B 701 " 0.076 2.00e-02 2.50e+03 pdb=" C7 FAD B 701 " -0.089 2.00e-02 2.50e+03 pdb=" C7M FAD B 701 " -0.214 2.00e-02 2.50e+03 pdb=" C8 FAD B 701 " -0.134 2.00e-02 2.50e+03 pdb=" C8M FAD B 701 " -0.303 2.00e-02 2.50e+03 pdb=" C9 FAD B 701 " -0.020 2.00e-02 2.50e+03 pdb=" C9A FAD B 701 " 0.144 2.00e-02 2.50e+03 pdb=" N1 FAD B 701 " -0.045 2.00e-02 2.50e+03 pdb=" N10 FAD B 701 " 0.270 2.00e-02 2.50e+03 pdb=" N3 FAD B 701 " -0.185 2.00e-02 2.50e+03 pdb=" N5 FAD B 701 " 0.321 2.00e-02 2.50e+03 pdb=" O2 FAD B 701 " -0.364 2.00e-02 2.50e+03 pdb=" O4 FAD B 701 " 0.003 2.00e-02 2.50e+03 ... (remaining 7653 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2755 2.72 - 3.26: 45634 3.26 - 3.81: 83778 3.81 - 4.35: 112687 4.35 - 4.90: 174977 Nonbonded interactions: 419831 Sorted by model distance: nonbonded pdb=" OD2 ASP F 308 " pdb=" OG1 THR F 564 " model vdw 2.173 3.040 nonbonded pdb=" OD2 ASP G 308 " pdb=" OG1 THR G 564 " model vdw 2.182 3.040 nonbonded pdb=" OD2 ASP D 308 " pdb=" OG1 THR D 564 " model vdw 2.184 3.040 nonbonded pdb=" OD2 ASP E 308 " pdb=" OG1 THR E 564 " model vdw 2.184 3.040 nonbonded pdb=" OD2 ASP H 308 " pdb=" OG1 THR H 564 " model vdw 2.185 3.040 ... (remaining 419826 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 6.060 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: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 45.050 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 : 0.003 0.076 43080 Z= 0.155 Angle : 0.524 5.811 58704 Z= 0.256 Chirality : 0.046 0.178 6184 Planarity : 0.008 0.197 7656 Dihedral : 10.318 89.906 15968 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.36 % Allowed : 4.27 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.71 (0.12), residues: 5280 helix: 0.92 (0.14), residues: 1504 sheet: -0.05 (0.20), residues: 712 loop : 0.53 (0.12), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 80 TYR 0.017 0.001 TYR B 395 PHE 0.018 0.001 PHE A 419 TRP 0.010 0.001 TRP G 566 HIS 0.005 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (43080) covalent geometry : angle 0.52353 / 0.26 (58704) hydrogen bonds : bond 0.21467 / 13.95 ( 1448) hydrogen bonds : angle 7.77917 / 5.57 ( 4278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 540 time to evaluate : 1.596 Fit side-chains REVERT: A 214 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7826 (ttm170) REVERT: A 259 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8237 (mtpt) REVERT: A 333 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7470 (mppt) REVERT: A 582 ILE cc_start: 0.8238 (mt) cc_final: 0.8032 (mt) REVERT: B 214 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7946 (ttm170) REVERT: B 236 VAL cc_start: 0.8634 (t) cc_final: 0.8184 (p) REVERT: B 259 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8194 (mtpt) REVERT: B 333 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7469 (mppt) REVERT: C 214 ARG cc_start: 0.8209 (ttm170) cc_final: 0.7955 (ttm170) REVERT: C 259 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8243 (mtpt) REVERT: C 333 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7503 (mppt) REVERT: C 582 ILE cc_start: 0.8201 (mt) cc_final: 0.7964 (mt) REVERT: D 214 ARG cc_start: 0.8281 (ttm170) cc_final: 0.8010 (ttm170) REVERT: D 259 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8232 (mtpt) REVERT: D 333 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7436 (mppt) REVERT: D 582 ILE cc_start: 0.8147 (mt) cc_final: 0.7943 (mt) REVERT: E 214 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7975 (ttm170) REVERT: E 259 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8243 (mtpt) REVERT: E 333 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7541 (mppt) REVERT: E 582 ILE cc_start: 0.8210 (mt) cc_final: 0.7968 (mt) REVERT: F 214 ARG cc_start: 0.8244 (ttm170) cc_final: 0.7961 (ttm170) REVERT: F 236 VAL cc_start: 0.8645 (t) cc_final: 0.8198 (p) REVERT: F 259 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8218 (mtpt) REVERT: F 333 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7497 (mppt) REVERT: F 582 ILE cc_start: 0.8194 (mt) cc_final: 0.7965 (mt) REVERT: G 214 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7997 (ttm170) REVERT: G 236 VAL cc_start: 0.8635 (t) cc_final: 0.8197 (p) REVERT: G 259 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8250 (mtpt) REVERT: G 333 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7497 (mppt) REVERT: H 214 ARG cc_start: 0.8279 (ttm170) cc_final: 0.8016 (ttm170) REVERT: H 259 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8215 (mtpt) REVERT: H 333 LYS cc_start: 0.8155 (mmmt) cc_final: 0.7554 (mppt) outliers start: 61 outliers final: 16 residues processed: 585 average time/residue: 0.8384 time to fit residues: 590.1152 Evaluate side-chains 408 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 392 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 515 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 265 optimal weight: 0.7980 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN A 480 HIS A 481 HIS B 170 GLN B 377 GLN B 480 HIS B 481 HIS C 58 ASN C 170 GLN C 377 GLN C 480 HIS C 481 HIS D 170 GLN D 377 GLN D 480 HIS D 481 HIS D 543 GLN E 170 GLN E 377 GLN E 480 HIS E 481 HIS F 58 ASN F 170 GLN F 377 GLN F 480 HIS F 481 HIS G 377 GLN G 480 HIS G 481 HIS H 170 GLN H 377 GLN H 480 HIS H 481 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.094059 restraints weight = 56490.308| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.47 r_work: 0.2988 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 43080 Z= 0.162 Angle : 0.576 7.743 58704 Z= 0.300 Chirality : 0.049 0.146 6184 Planarity : 0.005 0.048 7656 Dihedral : 5.964 56.525 6176 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.68 % Allowed : 6.95 % Favored : 91.37 % 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: 0.76 (0.12), residues: 5280 helix: 1.50 (0.15), residues: 1408 sheet: -0.14 (0.20), residues: 696 loop : 0.31 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 103 TYR 0.020 0.001 TYR C 395 PHE 0.022 0.002 PHE F 419 TRP 0.017 0.002 TRP A 566 HIS 0.004 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (43080) covalent geometry : angle 0.57606 / 0.30 (58704) hydrogen bonds : bond 0.04429 / 2.89 ( 1448) hydrogen bonds : angle 5.96327 / 4.25 ( 4278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 432 time to evaluate : 1.400 Fit side-chains REVERT: A 214 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7881 (ttm170) REVERT: A 236 VAL cc_start: 0.8638 (t) cc_final: 0.8194 (p) REVERT: A 259 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8325 (mtpt) REVERT: A 333 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7385 (mppt) REVERT: A 462 MET cc_start: 0.8811 (ttm) cc_final: 0.8547 (mtp) REVERT: A 548 LYS cc_start: 0.7980 (mptt) cc_final: 0.7334 (mppt) REVERT: B 214 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7858 (ttm170) REVERT: B 236 VAL cc_start: 0.8604 (t) cc_final: 0.8137 (p) REVERT: B 259 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8278 (mtpt) REVERT: B 333 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7410 (mppt) REVERT: B 462 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8542 (mtp) REVERT: B 548 LYS cc_start: 0.8014 (mptt) cc_final: 0.7359 (mppt) REVERT: C 214 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7857 (ttm170) REVERT: C 236 VAL cc_start: 0.8640 (t) cc_final: 0.8204 (p) REVERT: C 259 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8262 (mtpt) REVERT: C 462 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8569 (mtp) REVERT: C 548 LYS cc_start: 0.8034 (mptt) cc_final: 0.7364 (mppt) REVERT: C 644 ASP cc_start: 0.6933 (m-30) cc_final: 0.6727 (m-30) REVERT: D 214 ARG cc_start: 0.8254 (ttm170) cc_final: 0.7884 (ttm170) REVERT: D 236 VAL cc_start: 0.8618 (t) cc_final: 0.8175 (p) REVERT: D 259 LYS cc_start: 0.8736 (mtmm) cc_final: 0.8297 (mtpt) REVERT: D 332 ASP cc_start: 0.7453 (t0) cc_final: 0.7196 (t0) REVERT: D 462 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: D 548 LYS cc_start: 0.8012 (mptt) cc_final: 0.7348 (mppt) REVERT: D 644 ASP cc_start: 0.6876 (m-30) cc_final: 0.6649 (m-30) REVERT: E 214 ARG cc_start: 0.8254 (ttm170) cc_final: 0.7883 (ttm170) REVERT: E 233 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7196 (mm-30) REVERT: E 236 VAL cc_start: 0.8609 (t) cc_final: 0.8174 (p) REVERT: E 259 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8298 (mtpt) REVERT: E 333 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7438 (mppt) REVERT: E 462 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8567 (mtp) REVERT: E 644 ASP cc_start: 0.6924 (m-30) cc_final: 0.6704 (m-30) REVERT: F 214 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7869 (ttm170) REVERT: F 236 VAL cc_start: 0.8624 (t) cc_final: 0.8190 (p) REVERT: F 259 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8282 (mtpt) REVERT: F 333 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7437 (mppt) REVERT: F 462 MET cc_start: 0.8841 (ttm) cc_final: 0.8557 (mtp) REVERT: F 548 LYS cc_start: 0.8026 (mptt) cc_final: 0.7382 (mppt) REVERT: F 644 ASP cc_start: 0.6991 (m-30) cc_final: 0.6782 (m-30) REVERT: G 214 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7859 (ttm170) REVERT: G 236 VAL cc_start: 0.8583 (t) cc_final: 0.8142 (p) REVERT: G 259 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8279 (mtpt) REVERT: G 462 MET cc_start: 0.8834 (ttm) cc_final: 0.8562 (mtp) REVERT: G 548 LYS cc_start: 0.8014 (mptt) cc_final: 0.7378 (mppt) REVERT: G 644 ASP cc_start: 0.6908 (m-30) cc_final: 0.6682 (m-30) REVERT: H 214 ARG cc_start: 0.8257 (ttm170) cc_final: 0.7888 (ttm170) REVERT: H 236 VAL cc_start: 0.8583 (t) cc_final: 0.8147 (p) REVERT: H 259 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8325 (mtpt) REVERT: H 333 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7504 (mppt) REVERT: H 462 MET cc_start: 0.8829 (ttm) cc_final: 0.8539 (mtp) REVERT: H 548 LYS cc_start: 0.8026 (mptt) cc_final: 0.7378 (mppt) REVERT: H 644 ASP cc_start: 0.6895 (m-30) cc_final: 0.6669 (m-30) outliers start: 75 outliers final: 28 residues processed: 470 average time/residue: 0.7267 time to fit residues: 421.7300 Evaluate side-chains 404 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 462 MET Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 462 MET Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 515 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 21 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 383 optimal weight: 1.9990 chunk 426 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 237 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 433 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 543 GLN B 58 ASN B 543 GLN C 543 GLN E 543 GLN F 543 GLN G 543 GLN H 543 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092240 restraints weight = 56568.973| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.47 r_work: 0.2956 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43080 Z= 0.194 Angle : 0.599 8.019 58704 Z= 0.312 Chirality : 0.050 0.151 6184 Planarity : 0.005 0.042 7656 Dihedral : 6.154 56.761 6176 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.30 % Allowed : 7.33 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.50 (0.12), residues: 5280 helix: 1.22 (0.14), residues: 1456 sheet: -0.41 (0.18), residues: 776 loop : 0.21 (0.12), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 103 TYR 0.019 0.002 TYR C 395 PHE 0.023 0.002 PHE C 419 TRP 0.017 0.002 TRP D 566 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (43080) covalent geometry : angle 0.59938 / 0.31 (58704) hydrogen bonds : bond 0.04533 / 2.97 ( 1448) hydrogen bonds : angle 5.80944 / 4.14 ( 4278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 395 time to evaluate : 1.696 Fit side-chains REVERT: A 236 VAL cc_start: 0.8636 (t) cc_final: 0.8207 (p) REVERT: A 259 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8333 (mtpt) REVERT: A 333 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7417 (mppt) REVERT: A 418 HIS cc_start: 0.9396 (OUTLIER) cc_final: 0.9102 (m90) REVERT: A 462 MET cc_start: 0.8824 (ttm) cc_final: 0.8560 (mtp) REVERT: A 548 LYS cc_start: 0.7981 (mptt) cc_final: 0.7062 (mppt) REVERT: A 552 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8575 (mp) REVERT: B 213 MET cc_start: 0.9213 (mtp) cc_final: 0.9011 (mtm) REVERT: B 236 VAL cc_start: 0.8659 (t) cc_final: 0.8183 (p) REVERT: B 259 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8298 (mtpt) REVERT: B 333 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7428 (mppt) REVERT: B 418 HIS cc_start: 0.9391 (OUTLIER) cc_final: 0.9104 (m90) REVERT: B 548 LYS cc_start: 0.7998 (mptt) cc_final: 0.7069 (mppt) REVERT: B 552 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8580 (mp) REVERT: C 236 VAL cc_start: 0.8615 (t) cc_final: 0.8197 (p) REVERT: C 259 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8299 (mtpt) REVERT: C 333 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7515 (mppt) REVERT: C 418 HIS cc_start: 0.9390 (OUTLIER) cc_final: 0.9105 (m90) REVERT: C 548 LYS cc_start: 0.8016 (mptt) cc_final: 0.7082 (mppt) REVERT: C 552 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 644 ASP cc_start: 0.7052 (m-30) cc_final: 0.6809 (m-30) REVERT: D 213 MET cc_start: 0.9203 (mtp) cc_final: 0.8997 (mtm) REVERT: D 236 VAL cc_start: 0.8587 (t) cc_final: 0.8153 (p) REVERT: D 259 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8309 (mtpt) REVERT: D 332 ASP cc_start: 0.7624 (t0) cc_final: 0.7342 (t0) REVERT: D 418 HIS cc_start: 0.9398 (OUTLIER) cc_final: 0.9111 (m90) REVERT: D 462 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8576 (mtp) REVERT: D 548 LYS cc_start: 0.8021 (mptt) cc_final: 0.7078 (mppt) REVERT: D 552 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8574 (mp) REVERT: D 644 ASP cc_start: 0.7057 (m-30) cc_final: 0.6798 (m-30) REVERT: E 236 VAL cc_start: 0.8596 (t) cc_final: 0.8174 (p) REVERT: E 259 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8309 (mtpt) REVERT: E 333 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7453 (mppt) REVERT: E 418 HIS cc_start: 0.9408 (OUTLIER) cc_final: 0.9117 (m90) REVERT: E 462 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8535 (mtp) REVERT: E 552 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8585 (mp) REVERT: E 644 ASP cc_start: 0.7023 (m-30) cc_final: 0.6774 (m-30) REVERT: F 213 MET cc_start: 0.9202 (mtp) cc_final: 0.9000 (mtm) REVERT: F 236 VAL cc_start: 0.8622 (t) cc_final: 0.8192 (p) REVERT: F 259 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8322 (mtpt) REVERT: F 333 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7453 (mppt) REVERT: F 418 HIS cc_start: 0.9388 (OUTLIER) cc_final: 0.9102 (m90) REVERT: F 548 LYS cc_start: 0.8021 (mptt) cc_final: 0.7095 (mppt) REVERT: F 552 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8584 (mp) REVERT: F 644 ASP cc_start: 0.6962 (m-30) cc_final: 0.6736 (m-30) REVERT: G 213 MET cc_start: 0.9217 (mtp) cc_final: 0.9015 (mtm) REVERT: G 236 VAL cc_start: 0.8595 (t) cc_final: 0.8158 (p) REVERT: G 259 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8316 (mtpt) REVERT: G 333 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7499 (mppt) REVERT: G 418 HIS cc_start: 0.9392 (OUTLIER) cc_final: 0.9106 (m90) REVERT: G 548 LYS cc_start: 0.8011 (mptt) cc_final: 0.7089 (mppt) REVERT: G 552 ILE cc_start: 0.8988 (OUTLIER) cc_final: 0.8584 (mp) REVERT: G 644 ASP cc_start: 0.6970 (m-30) cc_final: 0.6755 (m-30) REVERT: H 213 MET cc_start: 0.9205 (mtp) cc_final: 0.9002 (mtm) REVERT: H 236 VAL cc_start: 0.8579 (t) cc_final: 0.8144 (p) REVERT: H 259 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8327 (mtpt) REVERT: H 333 LYS cc_start: 0.8178 (mmmt) cc_final: 0.7508 (mppt) REVERT: H 418 HIS cc_start: 0.9404 (OUTLIER) cc_final: 0.9113 (m90) REVERT: H 462 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8551 (mtp) REVERT: H 548 LYS cc_start: 0.8013 (mptt) cc_final: 0.7073 (mppt) REVERT: H 552 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8570 (mp) REVERT: H 644 ASP cc_start: 0.7006 (m-30) cc_final: 0.6741 (m-30) outliers start: 103 outliers final: 36 residues processed: 444 average time/residue: 0.6246 time to fit residues: 350.2469 Evaluate side-chains 442 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 385 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 456 MET Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 333 LYS Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 456 MET Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 530 THR Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 456 MET Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 582 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 313 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 343 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 352 optimal weight: 0.8980 chunk 286 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN G 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.096176 restraints weight = 56426.104| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.47 r_work: 0.3026 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 43080 Z= 0.105 Angle : 0.518 6.702 58704 Z= 0.267 Chirality : 0.046 0.136 6184 Planarity : 0.004 0.043 7656 Dihedral : 5.866 57.174 6176 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 8.77 % Favored : 89.40 % 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: 0.58 (0.12), residues: 5280 helix: 1.36 (0.14), residues: 1480 sheet: -0.46 (0.18), residues: 776 loop : 0.25 (0.12), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.019 0.001 TYR G 395 PHE 0.019 0.001 PHE A 419 TRP 0.020 0.002 TRP F 566 HIS 0.004 0.001 HIS F 567 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (43080) covalent geometry : angle 0.51756 / 0.27 (58704) hydrogen bonds : bond 0.03407 / 2.23 ( 1448) hydrogen bonds : angle 5.50380 / 3.92 ( 4278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 424 time to evaluate : 1.736 Fit side-chains REVERT: A 236 VAL cc_start: 0.8599 (t) cc_final: 0.8184 (p) REVERT: A 259 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8322 (mtpt) REVERT: A 333 LYS cc_start: 0.7972 (mmmt) cc_final: 0.7328 (mppt) REVERT: A 462 MET cc_start: 0.8728 (ttm) cc_final: 0.8503 (mtp) REVERT: A 548 LYS cc_start: 0.8009 (mptt) cc_final: 0.7125 (mppt) REVERT: A 552 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 121 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: B 236 VAL cc_start: 0.8667 (t) cc_final: 0.8185 (p) REVERT: B 259 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8315 (mtpt) REVERT: B 333 LYS cc_start: 0.7998 (mmmt) cc_final: 0.7373 (mppt) REVERT: B 548 LYS cc_start: 0.7964 (mptt) cc_final: 0.7073 (mppt) REVERT: B 552 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8563 (mp) REVERT: C 121 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: C 236 VAL cc_start: 0.8599 (t) cc_final: 0.8183 (p) REVERT: C 259 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8312 (mtpt) REVERT: C 548 LYS cc_start: 0.7983 (mptt) cc_final: 0.7084 (mppt) REVERT: C 552 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8562 (mp) REVERT: C 644 ASP cc_start: 0.6960 (m-30) cc_final: 0.6673 (m-30) REVERT: D 121 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: D 236 VAL cc_start: 0.8575 (t) cc_final: 0.8150 (p) REVERT: D 259 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8307 (mtpt) REVERT: D 332 ASP cc_start: 0.7522 (t0) cc_final: 0.7270 (t0) REVERT: D 462 MET cc_start: 0.8706 (ttm) cc_final: 0.8471 (mtp) REVERT: D 548 LYS cc_start: 0.7996 (mptt) cc_final: 0.7103 (mppt) REVERT: D 552 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8543 (mp) REVERT: D 644 ASP cc_start: 0.6956 (m-30) cc_final: 0.6676 (m-30) REVERT: E 236 VAL cc_start: 0.8555 (t) cc_final: 0.8146 (p) REVERT: E 259 LYS cc_start: 0.8754 (mtmm) cc_final: 0.8314 (mtpt) REVERT: E 333 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7385 (mppt) REVERT: E 462 MET cc_start: 0.8687 (ttm) cc_final: 0.8479 (mtp) REVERT: E 548 LYS cc_start: 0.7991 (mptt) cc_final: 0.7111 (mppt) REVERT: E 552 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8551 (mp) REVERT: E 644 ASP cc_start: 0.6931 (m-30) cc_final: 0.6668 (m-30) REVERT: F 121 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: F 236 VAL cc_start: 0.8594 (t) cc_final: 0.8177 (p) REVERT: F 259 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8324 (mtpt) REVERT: F 333 LYS cc_start: 0.8045 (mmmt) cc_final: 0.7408 (mppt) REVERT: F 548 LYS cc_start: 0.7966 (mptt) cc_final: 0.7077 (mppt) REVERT: F 552 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8570 (mp) REVERT: F 644 ASP cc_start: 0.6906 (m-30) cc_final: 0.6649 (m-30) REVERT: G 236 VAL cc_start: 0.8566 (t) cc_final: 0.8139 (p) REVERT: G 259 LYS cc_start: 0.8741 (mtmm) cc_final: 0.8293 (mtpt) REVERT: G 548 LYS cc_start: 0.7971 (mptt) cc_final: 0.7080 (mppt) REVERT: G 552 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8559 (mp) REVERT: G 644 ASP cc_start: 0.6893 (m-30) cc_final: 0.6636 (m-30) REVERT: H 236 VAL cc_start: 0.8577 (t) cc_final: 0.8157 (p) REVERT: H 259 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8324 (mtpt) REVERT: H 333 LYS cc_start: 0.8131 (mmmt) cc_final: 0.7469 (mppt) REVERT: H 462 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8456 (mtp) REVERT: H 548 LYS cc_start: 0.7959 (mptt) cc_final: 0.7050 (mppt) REVERT: H 552 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8545 (mp) REVERT: H 644 ASP cc_start: 0.6934 (m-30) cc_final: 0.6638 (m-30) outliers start: 82 outliers final: 40 residues processed: 465 average time/residue: 0.6581 time to fit residues: 384.3308 Evaluate side-chains 444 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 391 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 456 MET Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 568 CYS Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 456 MET Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 456 MET Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 552 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 162 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 472 optimal weight: 2.9990 chunk 245 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 308 optimal weight: 0.7980 chunk 432 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN B 286 HIS C 286 HIS D 286 HIS E 286 HIS H 286 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.110848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.094721 restraints weight = 56323.504| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.46 r_work: 0.3001 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43080 Z= 0.132 Angle : 0.542 7.324 58704 Z= 0.279 Chirality : 0.047 0.144 6184 Planarity : 0.004 0.041 7656 Dihedral : 5.916 57.176 6176 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.08 % Allowed : 9.73 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.12), residues: 5280 helix: 1.39 (0.14), residues: 1472 sheet: -0.63 (0.18), residues: 792 loop : 0.30 (0.12), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 103 TYR 0.019 0.001 TYR D 395 PHE 0.021 0.002 PHE H 419 TRP 0.016 0.002 TRP G 566 HIS 0.004 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (43080) covalent geometry : angle 0.54179 / 0.28 (58704) hydrogen bonds : bond 0.03659 / 2.40 ( 1448) hydrogen bonds : angle 5.48083 / 3.90 ( 4278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 415 time to evaluate : 1.461 Fit side-chains REVERT: A 236 VAL cc_start: 0.8592 (t) cc_final: 0.8177 (p) REVERT: A 259 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8323 (mtpt) REVERT: A 333 LYS cc_start: 0.7998 (mmmt) cc_final: 0.7345 (mppt) REVERT: A 462 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8529 (mtp) REVERT: A 548 LYS cc_start: 0.8010 (mptt) cc_final: 0.7101 (mppt) REVERT: A 552 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8581 (mp) REVERT: B 236 VAL cc_start: 0.8669 (t) cc_final: 0.8189 (p) REVERT: B 259 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8318 (mtpt) REVERT: B 333 LYS cc_start: 0.8027 (mmmt) cc_final: 0.7386 (mppt) REVERT: B 548 LYS cc_start: 0.8019 (mptt) cc_final: 0.7113 (mppt) REVERT: B 552 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 236 VAL cc_start: 0.8587 (t) cc_final: 0.8176 (p) REVERT: C 259 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8310 (mtpt) REVERT: C 333 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7484 (mppt) REVERT: C 548 LYS cc_start: 0.8035 (mptt) cc_final: 0.7122 (mppt) REVERT: C 552 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 644 ASP cc_start: 0.6957 (m-30) cc_final: 0.6665 (m-30) REVERT: D 236 VAL cc_start: 0.8576 (t) cc_final: 0.8154 (p) REVERT: D 259 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8305 (mtpt) REVERT: D 332 ASP cc_start: 0.7661 (t0) cc_final: 0.7378 (t0) REVERT: D 462 MET cc_start: 0.8757 (ttm) cc_final: 0.8542 (mtp) REVERT: D 548 LYS cc_start: 0.8028 (mptt) cc_final: 0.7104 (mppt) REVERT: D 552 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8564 (mp) REVERT: D 644 ASP cc_start: 0.6910 (m-30) cc_final: 0.6607 (m-30) REVERT: E 233 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7250 (mm-30) REVERT: E 236 VAL cc_start: 0.8583 (t) cc_final: 0.8176 (p) REVERT: E 259 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8303 (mtpt) REVERT: E 333 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7398 (mppt) REVERT: E 548 LYS cc_start: 0.8008 (mptt) cc_final: 0.7067 (mppt) REVERT: E 552 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8564 (mp) REVERT: E 644 ASP cc_start: 0.6936 (m-30) cc_final: 0.6640 (m-30) REVERT: F 236 VAL cc_start: 0.8582 (t) cc_final: 0.8165 (p) REVERT: F 259 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8330 (mtpt) REVERT: F 333 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7416 (mppt) REVERT: F 548 LYS cc_start: 0.8023 (mptt) cc_final: 0.7127 (mppt) REVERT: F 552 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8588 (mp) REVERT: G 236 VAL cc_start: 0.8569 (t) cc_final: 0.8147 (p) REVERT: G 259 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8314 (mtpt) REVERT: G 333 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7456 (mppt) REVERT: G 548 LYS cc_start: 0.8017 (mptt) cc_final: 0.7105 (mppt) REVERT: G 552 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8566 (mp) REVERT: G 644 ASP cc_start: 0.6864 (m-30) cc_final: 0.6631 (m-30) REVERT: H 236 VAL cc_start: 0.8560 (t) cc_final: 0.8147 (p) REVERT: H 259 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8330 (mtpt) REVERT: H 333 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7479 (mppt) REVERT: H 462 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8478 (mtp) REVERT: H 548 LYS cc_start: 0.8015 (mptt) cc_final: 0.7087 (mppt) REVERT: H 552 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8561 (mp) REVERT: H 644 ASP cc_start: 0.6950 (m-30) cc_final: 0.6651 (m-30) outliers start: 93 outliers final: 64 residues processed: 459 average time/residue: 0.6298 time to fit residues: 364.7667 Evaluate side-chains 484 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 408 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 286 HIS Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 333 LYS Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 286 HIS Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 456 MET Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 568 CYS Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 286 HIS Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 568 CYS Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 286 HIS Chi-restraints excluded: chain G residue 333 LYS Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 456 MET Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 286 HIS Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 456 MET Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 582 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 353 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 369 optimal weight: 8.9990 chunk 370 optimal weight: 3.9990 chunk 402 optimal weight: 7.9990 chunk 505 optimal weight: 0.4980 chunk 377 optimal weight: 2.9990 chunk 159 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 7.9990 chunk 361 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 58 ASN G 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.109577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.093363 restraints weight = 56457.281| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.47 r_work: 0.2978 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 43080 Z= 0.162 Angle : 0.572 7.958 58704 Z= 0.295 Chirality : 0.048 0.148 6184 Planarity : 0.004 0.041 7656 Dihedral : 6.024 56.887 6176 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.48 % Allowed : 9.97 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.12), residues: 5280 helix: 1.45 (0.15), residues: 1424 sheet: -0.52 (0.18), residues: 776 loop : 0.25 (0.11), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 103 TYR 0.019 0.001 TYR C 395 PHE 0.023 0.002 PHE F 419 TRP 0.018 0.002 TRP C 566 HIS 0.004 0.001 HIS H 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (43080) covalent geometry : angle 0.57195 / 0.29 (58704) hydrogen bonds : bond 0.03946 / 2.59 ( 1448) hydrogen bonds : angle 5.55359 / 3.96 ( 4278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 407 time to evaluate : 1.732 Fit side-chains REVERT: A 236 VAL cc_start: 0.8604 (t) cc_final: 0.8175 (p) REVERT: A 259 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8317 (mtpt) REVERT: A 333 LYS cc_start: 0.8036 (mmmt) cc_final: 0.7390 (mppt) REVERT: A 418 HIS cc_start: 0.9354 (OUTLIER) cc_final: 0.8975 (m90) REVERT: A 462 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8552 (mtp) REVERT: A 548 LYS cc_start: 0.8018 (mptt) cc_final: 0.7099 (mppt) REVERT: A 552 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8559 (mp) REVERT: B 236 VAL cc_start: 0.8654 (t) cc_final: 0.8167 (p) REVERT: B 259 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8306 (mtpt) REVERT: B 333 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7407 (mppt) REVERT: B 418 HIS cc_start: 0.9352 (OUTLIER) cc_final: 0.8970 (m90) REVERT: B 548 LYS cc_start: 0.8017 (mptt) cc_final: 0.7112 (mppt) REVERT: B 552 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8556 (mp) REVERT: C 236 VAL cc_start: 0.8603 (t) cc_final: 0.8181 (p) REVERT: C 259 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8307 (mtpt) REVERT: C 418 HIS cc_start: 0.9346 (OUTLIER) cc_final: 0.8967 (m90) REVERT: C 548 LYS cc_start: 0.8032 (mptt) cc_final: 0.7121 (mppt) REVERT: C 552 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8567 (mp) REVERT: C 644 ASP cc_start: 0.6942 (m-30) cc_final: 0.6638 (m-30) REVERT: D 236 VAL cc_start: 0.8600 (t) cc_final: 0.8167 (p) REVERT: D 259 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8296 (mtpt) REVERT: D 332 ASP cc_start: 0.7728 (t0) cc_final: 0.7488 (t0) REVERT: D 418 HIS cc_start: 0.9362 (OUTLIER) cc_final: 0.8999 (m90) REVERT: D 462 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: D 548 LYS cc_start: 0.8049 (mptt) cc_final: 0.7114 (mppt) REVERT: D 552 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8583 (mp) REVERT: D 644 ASP cc_start: 0.6943 (m-30) cc_final: 0.6626 (m-30) REVERT: E 236 VAL cc_start: 0.8582 (t) cc_final: 0.8162 (p) REVERT: E 259 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8305 (mtpt) REVERT: E 333 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7436 (mppt) REVERT: E 418 HIS cc_start: 0.9376 (OUTLIER) cc_final: 0.9007 (m90) REVERT: E 548 LYS cc_start: 0.8003 (mptt) cc_final: 0.7056 (mppt) REVERT: E 552 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8571 (mp) REVERT: E 644 ASP cc_start: 0.6926 (m-30) cc_final: 0.6615 (m-30) REVERT: F 236 VAL cc_start: 0.8592 (t) cc_final: 0.8157 (p) REVERT: F 259 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8315 (mtpt) REVERT: F 333 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7427 (mppt) REVERT: F 418 HIS cc_start: 0.9352 (OUTLIER) cc_final: 0.8969 (m90) REVERT: F 548 LYS cc_start: 0.8025 (mptt) cc_final: 0.7126 (mppt) REVERT: F 552 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8569 (mp) REVERT: G 236 VAL cc_start: 0.8590 (t) cc_final: 0.8155 (p) REVERT: G 259 LYS cc_start: 0.8761 (mtmm) cc_final: 0.8304 (mtpt) REVERT: G 418 HIS cc_start: 0.9359 (OUTLIER) cc_final: 0.8989 (m90) REVERT: G 548 LYS cc_start: 0.8024 (mptt) cc_final: 0.7115 (mppt) REVERT: G 552 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8536 (mp) REVERT: H 236 VAL cc_start: 0.8574 (t) cc_final: 0.8146 (p) REVERT: H 259 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8317 (mtpt) REVERT: H 333 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7508 (mppt) REVERT: H 418 HIS cc_start: 0.9365 (OUTLIER) cc_final: 0.8987 (m90) REVERT: H 462 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8505 (mtp) REVERT: H 548 LYS cc_start: 0.8020 (mptt) cc_final: 0.7090 (mppt) REVERT: H 552 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8544 (mp) REVERT: H 644 ASP cc_start: 0.6945 (m-30) cc_final: 0.6625 (m-30) outliers start: 111 outliers final: 59 residues processed: 473 average time/residue: 0.7239 time to fit residues: 429.0900 Evaluate side-chains 479 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 401 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 568 CYS Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 568 CYS Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 568 CYS Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 568 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 272 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 233 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 424 optimal weight: 7.9990 chunk 473 optimal weight: 10.0000 chunk 423 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 509 optimal weight: 0.9980 chunk 221 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092901 restraints weight = 56258.023| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.46 r_work: 0.2972 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 43080 Z= 0.176 Angle : 0.588 7.996 58704 Z= 0.302 Chirality : 0.049 0.149 6184 Planarity : 0.005 0.039 7656 Dihedral : 6.095 56.736 6176 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.62 % Allowed : 10.33 % Favored : 87.05 % 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: 0.50 (0.12), residues: 5280 helix: 1.40 (0.14), residues: 1424 sheet: -0.66 (0.18), residues: 792 loop : 0.21 (0.12), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 103 TYR 0.019 0.002 TYR E 395 PHE 0.023 0.002 PHE B 419 TRP 0.016 0.002 TRP A 566 HIS 0.004 0.001 HIS F 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (43080) covalent geometry : angle 0.58800 / 0.30 (58704) hydrogen bonds : bond 0.04056 / 2.66 ( 1448) hydrogen bonds : angle 5.59724 / 3.99 ( 4278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 395 time to evaluate : 1.307 Fit side-chains REVERT: A 236 VAL cc_start: 0.8615 (t) cc_final: 0.8183 (p) REVERT: A 259 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8315 (mtpt) REVERT: A 333 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7414 (mppt) REVERT: A 418 HIS cc_start: 0.9379 (OUTLIER) cc_final: 0.9076 (m90) REVERT: A 462 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8563 (mtp) REVERT: A 548 LYS cc_start: 0.8021 (mptt) cc_final: 0.7110 (mppt) REVERT: A 552 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 236 VAL cc_start: 0.8688 (t) cc_final: 0.8190 (p) REVERT: B 259 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8289 (mtpt) REVERT: B 333 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7439 (mppt) REVERT: B 418 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.9071 (m90) REVERT: B 548 LYS cc_start: 0.8006 (mptt) cc_final: 0.7110 (mppt) REVERT: B 552 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8546 (mp) REVERT: C 236 VAL cc_start: 0.8613 (t) cc_final: 0.8177 (p) REVERT: C 259 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8301 (mtpt) REVERT: C 418 HIS cc_start: 0.9372 (OUTLIER) cc_final: 0.9073 (m90) REVERT: C 548 LYS cc_start: 0.8040 (mptt) cc_final: 0.7125 (mppt) REVERT: C 552 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8549 (mp) REVERT: C 644 ASP cc_start: 0.6942 (m-30) cc_final: 0.6629 (m-30) REVERT: D 236 VAL cc_start: 0.8615 (t) cc_final: 0.8178 (p) REVERT: D 259 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8298 (mtpt) REVERT: D 332 ASP cc_start: 0.7764 (t0) cc_final: 0.7512 (t0) REVERT: D 418 HIS cc_start: 0.9381 (OUTLIER) cc_final: 0.9083 (m90) REVERT: D 462 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8578 (mtp) REVERT: D 548 LYS cc_start: 0.8029 (mptt) cc_final: 0.7104 (mppt) REVERT: D 552 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8532 (mp) REVERT: D 644 ASP cc_start: 0.6945 (m-30) cc_final: 0.6625 (m-30) REVERT: E 236 VAL cc_start: 0.8605 (t) cc_final: 0.8171 (p) REVERT: E 259 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8301 (mtpt) REVERT: E 333 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7452 (mppt) REVERT: E 418 HIS cc_start: 0.9393 (OUTLIER) cc_final: 0.9091 (m90) REVERT: E 548 LYS cc_start: 0.7995 (mptt) cc_final: 0.7054 (mppt) REVERT: E 552 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8541 (mp) REVERT: E 644 ASP cc_start: 0.6928 (m-30) cc_final: 0.6608 (m-30) REVERT: F 236 VAL cc_start: 0.8614 (t) cc_final: 0.8179 (p) REVERT: F 259 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8311 (mtpt) REVERT: F 333 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7455 (mppt) REVERT: F 418 HIS cc_start: 0.9376 (OUTLIER) cc_final: 0.9072 (m90) REVERT: F 548 LYS cc_start: 0.8022 (mptt) cc_final: 0.7123 (mppt) REVERT: F 552 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8563 (mp) REVERT: G 236 VAL cc_start: 0.8602 (t) cc_final: 0.8160 (p) REVERT: G 259 LYS cc_start: 0.8753 (mtmm) cc_final: 0.8300 (mtpt) REVERT: G 418 HIS cc_start: 0.9376 (OUTLIER) cc_final: 0.9076 (m90) REVERT: G 548 LYS cc_start: 0.8010 (mptt) cc_final: 0.7106 (mppt) REVERT: G 552 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8544 (mp) REVERT: H 236 VAL cc_start: 0.8605 (t) cc_final: 0.8172 (p) REVERT: H 259 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8306 (mtpt) REVERT: H 333 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7526 (mppt) REVERT: H 418 HIS cc_start: 0.9386 (OUTLIER) cc_final: 0.9084 (m90) REVERT: H 462 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8539 (mtp) REVERT: H 548 LYS cc_start: 0.8033 (mptt) cc_final: 0.7100 (mppt) REVERT: H 552 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8533 (mp) REVERT: H 644 ASP cc_start: 0.6951 (m-30) cc_final: 0.6631 (m-30) outliers start: 117 outliers final: 74 residues processed: 464 average time/residue: 0.5759 time to fit residues: 336.2619 Evaluate side-chains 483 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 390 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 568 CYS Chi-restraints excluded: chain E residue 582 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 568 CYS Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 530 THR Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 568 CYS Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 582 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 479 optimal weight: 7.9990 chunk 375 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 368 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.094250 restraints weight = 56470.642| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.47 r_work: 0.2991 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43080 Z= 0.139 Angle : 0.558 7.575 58704 Z= 0.285 Chirality : 0.047 0.143 6184 Planarity : 0.004 0.041 7656 Dihedral : 6.000 56.977 6176 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.46 % Allowed : 10.93 % Favored : 86.61 % 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: 0.53 (0.12), residues: 5280 helix: 1.46 (0.14), residues: 1424 sheet: -0.67 (0.18), residues: 792 loop : 0.21 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.019 0.001 TYR H 395 PHE 0.021 0.002 PHE D 419 TRP 0.017 0.002 TRP F 566 HIS 0.004 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (43080) covalent geometry : angle 0.55844 / 0.28 (58704) hydrogen bonds : bond 0.03688 / 2.42 ( 1448) hydrogen bonds : angle 5.49663 / 3.92 ( 4278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 405 time to evaluate : 1.097 Fit side-chains REVERT: A 236 VAL cc_start: 0.8591 (t) cc_final: 0.8165 (p) REVERT: A 259 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8320 (mtpt) REVERT: A 333 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7392 (mppt) REVERT: A 462 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8529 (mtp) REVERT: A 548 LYS cc_start: 0.8015 (mptt) cc_final: 0.7107 (mppt) REVERT: A 552 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 236 VAL cc_start: 0.8685 (t) cc_final: 0.8184 (p) REVERT: B 259 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8306 (mtpt) REVERT: B 333 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7424 (mppt) REVERT: B 548 LYS cc_start: 0.8022 (mptt) cc_final: 0.7125 (mppt) REVERT: B 552 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8569 (mp) REVERT: C 236 VAL cc_start: 0.8600 (t) cc_final: 0.8176 (p) REVERT: C 259 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8305 (mtpt) REVERT: C 456 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8656 (mtp) REVERT: C 548 LYS cc_start: 0.8030 (mptt) cc_final: 0.7121 (mppt) REVERT: C 552 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 644 ASP cc_start: 0.6942 (m-30) cc_final: 0.6625 (m-30) REVERT: D 236 VAL cc_start: 0.8584 (t) cc_final: 0.8153 (p) REVERT: D 259 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8303 (mtpt) REVERT: D 332 ASP cc_start: 0.7743 (t0) cc_final: 0.7503 (t0) REVERT: D 462 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.8513 (mtp) REVERT: D 548 LYS cc_start: 0.8044 (mptt) cc_final: 0.7113 (mppt) REVERT: D 552 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8568 (mp) REVERT: D 644 ASP cc_start: 0.6919 (m-30) cc_final: 0.6600 (m-30) REVERT: E 236 VAL cc_start: 0.8577 (t) cc_final: 0.8148 (p) REVERT: E 259 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8308 (mtpt) REVERT: E 333 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7442 (mppt) REVERT: E 548 LYS cc_start: 0.7981 (mptt) cc_final: 0.7046 (mppt) REVERT: E 552 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8573 (mp) REVERT: E 644 ASP cc_start: 0.6938 (m-30) cc_final: 0.6617 (m-30) REVERT: F 236 VAL cc_start: 0.8598 (t) cc_final: 0.8164 (p) REVERT: F 259 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8312 (mtpt) REVERT: F 333 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7434 (mppt) REVERT: F 456 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8640 (mtp) REVERT: F 548 LYS cc_start: 0.8020 (mptt) cc_final: 0.7127 (mppt) REVERT: F 552 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8590 (mp) REVERT: G 236 VAL cc_start: 0.8584 (t) cc_final: 0.8143 (p) REVERT: G 259 LYS cc_start: 0.8754 (mtmm) cc_final: 0.8307 (mtpt) REVERT: G 548 LYS cc_start: 0.8017 (mptt) cc_final: 0.7116 (mppt) REVERT: G 552 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8579 (mp) REVERT: H 236 VAL cc_start: 0.8577 (t) cc_final: 0.8139 (p) REVERT: H 259 LYS cc_start: 0.8749 (mtmm) cc_final: 0.8315 (mtpt) REVERT: H 333 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7512 (mppt) REVERT: H 456 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8671 (mtp) REVERT: H 462 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8493 (mtp) REVERT: H 548 LYS cc_start: 0.8030 (mptt) cc_final: 0.7102 (mppt) REVERT: H 552 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8560 (mp) REVERT: H 644 ASP cc_start: 0.6940 (m-30) cc_final: 0.6623 (m-30) outliers start: 110 outliers final: 80 residues processed: 474 average time/residue: 0.4601 time to fit residues: 276.6710 Evaluate side-chains 484 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 390 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 582 ILE Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 568 CYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 456 MET Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 568 CYS Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 644 ASP Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 530 THR Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 568 CYS Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 644 ASP Chi-restraints excluded: chain G residue 652 LEU Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 456 MET Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 652 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 315 optimal weight: 9.9990 chunk 174 optimal weight: 8.9990 chunk 73 optimal weight: 1.9990 chunk 382 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 236 optimal weight: 2.9990 chunk 498 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096036 restraints weight = 56222.127| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.47 r_work: 0.3023 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43080 Z= 0.113 Angle : 0.538 6.649 58704 Z= 0.275 Chirality : 0.046 0.144 6184 Planarity : 0.004 0.043 7656 Dihedral : 5.873 57.513 6176 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 11.34 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 5280 helix: 1.35 (0.14), residues: 1480 sheet: -0.65 (0.18), residues: 792 loop : 0.28 (0.12), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 577 TYR 0.020 0.001 TYR A 395 PHE 0.019 0.001 PHE F 419 TRP 0.023 0.002 TRP F 566 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (43080) covalent geometry : angle 0.53830 / 0.27 (58704) hydrogen bonds : bond 0.03340 / 2.19 ( 1448) hydrogen bonds : angle 5.37862 / 3.83 ( 4278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 395 time to evaluate : 1.036 Fit side-chains REVERT: A 236 VAL cc_start: 0.8575 (t) cc_final: 0.8158 (p) REVERT: A 259 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8322 (mtpt) REVERT: A 333 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7383 (mppt) REVERT: A 462 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8503 (mtp) REVERT: A 548 LYS cc_start: 0.7956 (mptt) cc_final: 0.7070 (mppt) REVERT: A 552 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8565 (mp) REVERT: B 236 VAL cc_start: 0.8673 (t) cc_final: 0.8176 (p) REVERT: B 259 LYS cc_start: 0.8704 (mtmm) cc_final: 0.8311 (mtpt) REVERT: B 333 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7419 (mppt) REVERT: B 548 LYS cc_start: 0.7991 (mptt) cc_final: 0.7097 (mppt) REVERT: B 552 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8553 (mp) REVERT: C 236 VAL cc_start: 0.8566 (t) cc_final: 0.8152 (p) REVERT: C 259 LYS cc_start: 0.8746 (mtmm) cc_final: 0.8313 (mtpt) REVERT: C 548 LYS cc_start: 0.8009 (mptt) cc_final: 0.7114 (mppt) REVERT: C 552 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8565 (mp) REVERT: D 236 VAL cc_start: 0.8560 (t) cc_final: 0.8138 (p) REVERT: D 259 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8311 (mtpt) REVERT: D 332 ASP cc_start: 0.7709 (t0) cc_final: 0.7469 (t0) REVERT: D 548 LYS cc_start: 0.7999 (mptt) cc_final: 0.7083 (mppt) REVERT: D 552 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8546 (mp) REVERT: E 236 VAL cc_start: 0.8548 (t) cc_final: 0.8130 (p) REVERT: E 259 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8305 (mtpt) REVERT: E 333 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7454 (mppt) REVERT: E 548 LYS cc_start: 0.7962 (mptt) cc_final: 0.7041 (mppt) REVERT: E 552 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8546 (mp) REVERT: F 236 VAL cc_start: 0.8559 (t) cc_final: 0.8138 (p) REVERT: F 259 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8317 (mtpt) REVERT: F 333 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7433 (mppt) REVERT: F 548 LYS cc_start: 0.7992 (mptt) cc_final: 0.7107 (mppt) REVERT: F 552 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8565 (mp) REVERT: G 236 VAL cc_start: 0.8540 (t) cc_final: 0.8112 (p) REVERT: G 259 LYS cc_start: 0.8748 (mtmm) cc_final: 0.8309 (mtpt) REVERT: G 548 LYS cc_start: 0.7996 (mptt) cc_final: 0.7097 (mppt) REVERT: G 552 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8554 (mp) REVERT: H 236 VAL cc_start: 0.8558 (t) cc_final: 0.8144 (p) REVERT: H 259 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8320 (mtpt) REVERT: H 333 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7524 (mppt) REVERT: H 462 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8455 (mtp) REVERT: H 548 LYS cc_start: 0.7996 (mptt) cc_final: 0.7079 (mppt) REVERT: H 552 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8551 (mp) outliers start: 111 outliers final: 77 residues processed: 464 average time/residue: 0.4329 time to fit residues: 258.6699 Evaluate side-chains 470 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 383 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 568 CYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 568 CYS Chi-restraints excluded: chain F residue 582 ILE Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 568 CYS Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 652 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 652 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 64 optimal weight: 10.0000 chunk 427 optimal weight: 2.9990 chunk 444 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 515 optimal weight: 0.5980 chunk 411 optimal weight: 0.9980 chunk 492 optimal weight: 2.9990 chunk 372 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.096798 restraints weight = 56305.725| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.47 r_work: 0.3035 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 43080 Z= 0.107 Angle : 0.523 6.576 58704 Z= 0.269 Chirality : 0.046 0.138 6184 Planarity : 0.004 0.043 7656 Dihedral : 5.811 58.151 6176 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.15 % Allowed : 11.81 % Favored : 86.05 % 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: 0.66 (0.12), residues: 5280 helix: 1.48 (0.15), residues: 1472 sheet: -0.49 (0.19), residues: 776 loop : 0.29 (0.12), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.020 0.001 TYR B 395 PHE 0.019 0.001 PHE B 419 TRP 0.023 0.002 TRP G 566 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (43080) covalent geometry : angle 0.52320 / 0.27 (58704) hydrogen bonds : bond 0.03232 / 2.11 ( 1448) hydrogen bonds : angle 5.30474 / 3.78 ( 4278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 388 time to evaluate : 0.943 Fit side-chains REVERT: A 236 VAL cc_start: 0.8563 (t) cc_final: 0.8148 (p) REVERT: A 259 LYS cc_start: 0.8743 (mtmm) cc_final: 0.8315 (mtpt) REVERT: A 333 LYS cc_start: 0.8039 (mmmt) cc_final: 0.7401 (mppt) REVERT: A 462 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8482 (mtp) REVERT: A 548 LYS cc_start: 0.7929 (mptt) cc_final: 0.7032 (mppt) REVERT: A 552 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 236 VAL cc_start: 0.8615 (t) cc_final: 0.8122 (p) REVERT: B 259 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8315 (mtpt) REVERT: B 333 LYS cc_start: 0.8027 (mmmt) cc_final: 0.7429 (mppt) REVERT: B 548 LYS cc_start: 0.7957 (mptt) cc_final: 0.7073 (mppt) REVERT: B 552 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8540 (mp) REVERT: C 236 VAL cc_start: 0.8546 (t) cc_final: 0.8131 (p) REVERT: C 259 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8308 (mtpt) REVERT: C 548 LYS cc_start: 0.7977 (mptt) cc_final: 0.7091 (mppt) REVERT: C 552 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8556 (mp) REVERT: D 236 VAL cc_start: 0.8568 (t) cc_final: 0.8154 (p) REVERT: D 259 LYS cc_start: 0.8725 (mtmm) cc_final: 0.8302 (mtpt) REVERT: D 332 ASP cc_start: 0.7724 (t0) cc_final: 0.7450 (t0) REVERT: D 548 LYS cc_start: 0.7939 (mptt) cc_final: 0.7044 (mppt) REVERT: D 552 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8535 (mp) REVERT: E 236 VAL cc_start: 0.8558 (t) cc_final: 0.8149 (p) REVERT: E 259 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8295 (mtpt) REVERT: E 333 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7448 (mppt) REVERT: E 548 LYS cc_start: 0.7953 (mptt) cc_final: 0.7036 (mppt) REVERT: E 552 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8537 (mp) REVERT: F 236 VAL cc_start: 0.8542 (t) cc_final: 0.8128 (p) REVERT: F 259 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8313 (mtpt) REVERT: F 333 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7429 (mppt) REVERT: F 548 LYS cc_start: 0.7969 (mptt) cc_final: 0.7098 (mppt) REVERT: F 552 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8556 (mp) REVERT: G 236 VAL cc_start: 0.8529 (t) cc_final: 0.8106 (p) REVERT: G 259 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8295 (mtpt) REVERT: G 548 LYS cc_start: 0.7956 (mptt) cc_final: 0.7066 (mppt) REVERT: G 552 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8545 (mp) REVERT: H 236 VAL cc_start: 0.8556 (t) cc_final: 0.8149 (p) REVERT: H 259 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8321 (mtpt) REVERT: H 333 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7532 (mppt) REVERT: H 462 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8469 (mtp) REVERT: H 548 LYS cc_start: 0.7933 (mptt) cc_final: 0.7035 (mppt) REVERT: H 552 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8536 (mp) outliers start: 96 outliers final: 78 residues processed: 451 average time/residue: 0.4131 time to fit residues: 235.1943 Evaluate side-chains 460 residues out of total 4472 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 372 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain B residue 524 LYS Chi-restraints excluded: chain B residue 552 ILE Chi-restraints excluded: chain B residue 568 CYS Chi-restraints excluded: chain B residue 652 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 552 ILE Chi-restraints excluded: chain C residue 568 CYS Chi-restraints excluded: chain C residue 652 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 568 CYS Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 552 ILE Chi-restraints excluded: chain E residue 568 CYS Chi-restraints excluded: chain E residue 652 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 121 GLU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 552 ILE Chi-restraints excluded: chain F residue 568 CYS Chi-restraints excluded: chain F residue 652 LEU Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 121 GLU Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain G residue 552 ILE Chi-restraints excluded: chain G residue 568 CYS Chi-restraints excluded: chain G residue 582 ILE Chi-restraints excluded: chain G residue 652 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 120 ASP Chi-restraints excluded: chain H residue 121 GLU Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 462 MET Chi-restraints excluded: chain H residue 515 HIS Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 552 ILE Chi-restraints excluded: chain H residue 568 CYS Chi-restraints excluded: chain H residue 652 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 195 optimal weight: 0.8980 chunk 74 optimal weight: 0.0060 chunk 351 optimal weight: 5.9990 chunk 410 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 226 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 308 optimal weight: 0.8980 chunk 418 optimal weight: 6.9990 chunk 180 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN H 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.113600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097890 restraints weight = 56968.323| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.46 r_work: 0.3056 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 43080 Z= 0.099 Angle : 0.515 6.320 58704 Z= 0.263 Chirality : 0.046 0.137 6184 Planarity : 0.004 0.043 7656 Dihedral : 5.738 58.990 6176 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.90 % Allowed : 11.90 % Favored : 86.20 % 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: 0.71 (0.12), residues: 5280 helix: 1.50 (0.15), residues: 1472 sheet: -0.47 (0.19), residues: 776 loop : 0.33 (0.12), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 128 TYR 0.020 0.001 TYR H 395 PHE 0.018 0.001 PHE G 419 TRP 0.024 0.002 TRP G 566 HIS 0.003 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (43080) covalent geometry : angle 0.51474 / 0.26 (58704) hydrogen bonds : bond 0.03087 / 2.01 ( 1448) hydrogen bonds : angle 5.22995 / 3.73 ( 4278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12436.89 seconds wall clock time: 213 minutes 38.70 seconds (12818.70 seconds total)