Starting phenix.real_space_refine on Fri Feb 6 03:21:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l41_62802/02_2026/9l41_62802.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l41_62802/02_2026/9l41_62802.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l41_62802/02_2026/9l41_62802.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l41_62802/02_2026/9l41_62802.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l41_62802/02_2026/9l41_62802.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l41_62802/02_2026/9l41_62802.map" } resolution = 2.99 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= 0.087 sd= 0.845 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14004 2.51 5 N 3768 2.21 5 O 4152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22059 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 28, 'TRANS': 389} Chain: "R" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 772 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 91} Chain: "C" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "D" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 28, 'TRANS': 389} Chain: "S" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 772 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 91} Chain: "E" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3321 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 411} Chain: "F" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 28, 'TRANS': 389} Chain: "T" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 772 Classifications: {'peptide': 96} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 91} Time building chain proxies: 5.08, per 1000 atoms: 0.23 Number of scatterers: 22059 At special positions: 0 Unit cell: (167.2, 163.9, 165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 4152 8.00 N 3768 7.00 C 14004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.05 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.05 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.02 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 128 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 29 " distance=2.04 Simple disulfide: pdb=" SG CYS B 95 " - pdb=" SG CYS B 109 " distance=2.03 Simple disulfide: pdb=" SG CYS B 156 " - pdb=" SG CYS B 270 " distance=2.05 Simple disulfide: pdb=" SG CYS B 205 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 224 " distance=2.03 Simple disulfide: pdb=" SG CYS R 67 " - pdb=" SG CYS R 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.05 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.05 Simple disulfide: pdb=" SG CYS C 259 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 301 " - pdb=" SG CYS C 376 " distance=2.02 Simple disulfide: pdb=" SG CYS C 306 " - pdb=" SG CYS C 380 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 370 " distance=2.02 Simple disulfide: pdb=" SG CYS D 20 " - pdb=" SG CYS D 128 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 29 " distance=2.04 Simple disulfide: pdb=" SG CYS D 95 " - pdb=" SG CYS D 109 " distance=2.03 Simple disulfide: pdb=" SG CYS D 156 " - pdb=" SG CYS D 270 " distance=2.05 Simple disulfide: pdb=" SG CYS D 205 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 207 " - pdb=" SG CYS D 224 " distance=2.03 Simple disulfide: pdb=" SG CYS S 67 " - pdb=" SG CYS S 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.05 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.02 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.02 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.02 Simple disulfide: pdb=" SG CYS F 20 " - pdb=" SG CYS F 128 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 29 " distance=2.04 Simple disulfide: pdb=" SG CYS F 95 " - pdb=" SG CYS F 109 " distance=2.02 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 270 " distance=2.05 Simple disulfide: pdb=" SG CYS F 205 " - pdb=" SG CYS F 230 " distance=2.03 Simple disulfide: pdb=" SG CYS F 207 " - pdb=" SG CYS F 224 " distance=2.03 Simple disulfide: pdb=" SG CYS T 67 " - pdb=" SG CYS T 73 " distance=2.04 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: 1.65 Conformation dependent library (CDL) restraints added in 745.8 milliseconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5340 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 69 sheets defined 15.1% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.538A pdb=" N ASN A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 254 removed outlier: 3.535A pdb=" N GLU A 253 " --> pdb=" O PRO A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 removed outlier: 3.735A pdb=" N ALA A 286 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.647A pdb=" N ALA A 401 " --> pdb=" O PHE A 398 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL A 402 " --> pdb=" O GLN A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 398 through 402' Processing helix chain 'A' and resid 403 through 438 removed outlier: 3.684A pdb=" N VAL A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.595A pdb=" N LEU B 12 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 13 " --> pdb=" O PHE B 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 9 through 13' Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.748A pdb=" N ILE B 360 " --> pdb=" O PRO B 356 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 361 " --> pdb=" O HIS B 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'B' and resid 374 through 405 removed outlier: 3.594A pdb=" N LEU B 383 " --> pdb=" O ALA B 379 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 396 " --> pdb=" O CYS B 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'R' and resid 18 through 24 Processing helix chain 'R' and resid 29 through 34 removed outlier: 3.608A pdb=" N ARG R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 29 through 34' Processing helix chain 'R' and resid 62 through 67 Processing helix chain 'C' and resid 238 through 246 removed outlier: 3.538A pdb=" N ASN C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C 246 " --> pdb=" O MET C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 removed outlier: 3.536A pdb=" N GLU C 253 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 287 removed outlier: 3.735A pdb=" N ALA C 286 " --> pdb=" O PRO C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 402 removed outlier: 3.649A pdb=" N ALA C 401 " --> pdb=" O PHE C 398 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL C 402 " --> pdb=" O GLN C 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 398 through 402' Processing helix chain 'C' and resid 403 through 438 removed outlier: 3.684A pdb=" N VAL C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 13 removed outlier: 3.596A pdb=" N LEU D 12 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 13 " --> pdb=" O PHE D 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 9 through 13' Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 355 through 367 removed outlier: 3.749A pdb=" N ILE D 360 " --> pdb=" O PRO D 356 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE D 361 " --> pdb=" O HIS D 357 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 405 removed outlier: 3.594A pdb=" N LEU D 383 " --> pdb=" O ALA D 379 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 390 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 394 " --> pdb=" O ALA D 390 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 396 " --> pdb=" O CYS D 392 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG D 397 " --> pdb=" O ILE D 393 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'D' and resid 413 through 418 Processing helix chain 'S' and resid 18 through 24 Processing helix chain 'S' and resid 29 through 34 removed outlier: 3.607A pdb=" N ARG S 33 " --> pdb=" O LYS S 29 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY S 34 " --> pdb=" O LEU S 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 29 through 34' Processing helix chain 'S' and resid 62 through 67 Processing helix chain 'E' and resid 238 through 246 removed outlier: 3.538A pdb=" N ASN E 245 " --> pdb=" O GLU E 241 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN E 246 " --> pdb=" O MET E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 254 removed outlier: 3.536A pdb=" N GLU E 253 " --> pdb=" O PRO E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 removed outlier: 3.735A pdb=" N ALA E 286 " --> pdb=" O PRO E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 402 removed outlier: 3.648A pdb=" N ALA E 401 " --> pdb=" O PHE E 398 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL E 402 " --> pdb=" O GLN E 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 398 through 402' Processing helix chain 'E' and resid 403 through 438 removed outlier: 3.684A pdb=" N VAL E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU E 428 " --> pdb=" O GLY E 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 13 removed outlier: 3.595A pdb=" N LEU F 12 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 13 " --> pdb=" O PHE F 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 9 through 13' Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 355 through 367 removed outlier: 3.749A pdb=" N ILE F 360 " --> pdb=" O PRO F 356 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE F 361 " --> pdb=" O HIS F 357 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 372 Processing helix chain 'F' and resid 374 through 405 removed outlier: 3.594A pdb=" N LEU F 383 " --> pdb=" O ALA F 379 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F 390 " --> pdb=" O THR F 386 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA F 396 " --> pdb=" O CYS F 392 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG F 397 " --> pdb=" O ILE F 393 " (cutoff:3.500A) Proline residue: F 403 - end of helix Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'T' and resid 18 through 24 Processing helix chain 'T' and resid 29 through 34 removed outlier: 3.609A pdb=" N ARG T 33 " --> pdb=" O LYS T 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY T 34 " --> pdb=" O LEU T 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 29 through 34' Processing helix chain 'T' and resid 62 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.882A pdb=" N LYS A 160 " --> pdb=" O ASP A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.687A pdb=" N GLY A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 36 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 130 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 38 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS A 44 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 122 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A 46 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 4.708A pdb=" N VAL A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR A 46 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU A 122 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS A 44 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA A 128 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 38 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 130 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 36 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.937A pdb=" N GLN A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.531A pdb=" N GLN A 102 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 79 " --> pdb=" O SER A 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 106 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA8, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.527A pdb=" N ARG A 220 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 303 removed outlier: 3.872A pdb=" N ILE A 352 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 350 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 330 through 332 Processing sheet with id=AB2, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB3, first strand: chain 'A' and resid 362 through 363 Processing sheet with id=AB4, first strand: chain 'A' and resid 387 through 388 removed outlier: 5.768A pdb=" N ARG B 295 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE B 315 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR B 297 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B 313 " --> pdb=" O THR B 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 18 through 20 Processing sheet with id=AB6, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.885A pdb=" N GLN B 50 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 38 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG B 48 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N SER B 52 " --> pdb=" O MET B 71 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET B 71 " --> pdb=" O SER B 52 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS B 67 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 39 removed outlier: 6.885A pdb=" N GLN B 50 " --> pdb=" O GLU B 36 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL B 38 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG B 48 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 11.897A pdb=" N ILE B 49 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N GLN B 108 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N VAL B 51 " --> pdb=" O LEU B 106 " (cutoff:3.500A) removed outlier: 11.602A pdb=" N LEU B 106 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA B 53 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N PHE B 104 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N TYR B 57 " --> pdb=" O HIS B 100 " (cutoff:3.500A) removed outlier: 12.531A pdb=" N HIS B 100 " --> pdb=" O TYR B 57 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 87 through 90 removed outlier: 3.614A pdb=" N SER B 114 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 132 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR B 116 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N VAL B 130 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 152 through 159 Processing sheet with id=AC1, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.946A pdb=" N GLY B 257 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 184 through 187 removed outlier: 4.659A pdb=" N VAL B 191 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 219 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 210 through 215 removed outlier: 3.608A pdb=" N GLY B 213 " --> pdb=" O TYR B 203 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 201 " --> pdb=" O VAL B 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 279 through 283 removed outlier: 3.653A pdb=" N THR B 279 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 283 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 286 " --> pdb=" O TRP B 283 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 3 through 6 Processing sheet with id=AC6, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.882A pdb=" N LYS C 160 " --> pdb=" O ASP C 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 15 through 19 removed outlier: 6.686A pdb=" N GLY C 132 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER C 36 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS C 130 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU C 38 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR C 42 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 124 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 44 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 122 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR C 46 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 140 through 147 removed outlier: 4.710A pdb=" N VAL C 120 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR C 46 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU C 122 " --> pdb=" O LYS C 44 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS C 44 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 124 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR C 42 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR C 126 " --> pdb=" O PRO C 40 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ALA C 128 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LEU C 38 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS C 130 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER C 36 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY C 132 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.940A pdb=" N GLN C 59 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.530A pdb=" N GLN C 102 " --> pdb=" O PHE C 81 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 79 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 106 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AD3, first strand: chain 'C' and resid 203 through 204 Processing sheet with id=AD4, first strand: chain 'C' and resid 220 through 221 removed outlier: 3.527A pdb=" N ARG C 220 " --> pdb=" O THR C 234 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 301 through 303 removed outlier: 3.871A pdb=" N ILE C 352 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 350 " --> pdb=" O TYR C 320 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 330 through 332 Processing sheet with id=AD7, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AD8, first strand: chain 'C' and resid 362 through 363 Processing sheet with id=AD9, first strand: chain 'C' and resid 387 through 388 removed outlier: 5.767A pdb=" N ARG D 295 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE D 315 " --> pdb=" O ARG D 295 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR D 297 " --> pdb=" O GLU D 313 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU D 313 " --> pdb=" O THR D 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 18 through 20 Processing sheet with id=AE2, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.886A pdb=" N GLN D 50 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 38 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 10.703A pdb=" N SER D 52 " --> pdb=" O MET D 71 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET D 71 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS D 67 " --> pdb=" O GLY D 56 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.886A pdb=" N GLN D 50 " --> pdb=" O GLU D 36 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL D 38 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ARG D 48 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ILE D 49 " --> pdb=" O GLN D 108 " (cutoff:3.500A) removed outlier: 11.375A pdb=" N GLN D 108 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 11.885A pdb=" N VAL D 51 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N LEU D 106 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ALA D 53 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N PHE D 104 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR D 57 " --> pdb=" O HIS D 100 " (cutoff:3.500A) removed outlier: 12.530A pdb=" N HIS D 100 " --> pdb=" O TYR D 57 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 87 through 90 removed outlier: 3.613A pdb=" N SER D 114 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LYS D 132 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR D 116 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL D 130 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 152 through 159 Processing sheet with id=AE6, first strand: chain 'D' and resid 241 through 242 removed outlier: 3.945A pdb=" N GLY D 257 " --> pdb=" O MET D 172 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 184 through 187 removed outlier: 4.659A pdb=" N VAL D 191 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 219 " --> pdb=" O ILE D 193 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 210 through 215 removed outlier: 3.608A pdb=" N GLY D 213 " --> pdb=" O TYR D 203 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL D 201 " --> pdb=" O VAL D 215 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 279 through 283 removed outlier: 3.656A pdb=" N THR D 279 " --> pdb=" O HIS D 290 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP D 283 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 286 " --> pdb=" O TRP D 283 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 3 through 6 Processing sheet with id=AF2, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.884A pdb=" N LYS E 160 " --> pdb=" O ASP E 281 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 15 through 19 removed outlier: 6.686A pdb=" N GLY E 132 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER E 36 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS E 130 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU E 38 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA E 128 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR E 126 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR E 42 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL E 124 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS E 44 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU E 122 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR E 46 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 120 " --> pdb=" O TYR E 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 140 through 147 removed outlier: 4.709A pdb=" N VAL E 120 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR E 46 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU E 122 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LYS E 44 " --> pdb=" O LEU E 122 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL E 124 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR E 42 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR E 126 " --> pdb=" O PRO E 40 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA E 128 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU E 38 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS E 130 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N SER E 36 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLY E 132 " --> pdb=" O VAL E 34 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.936A pdb=" N GLN E 59 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.531A pdb=" N GLN E 102 " --> pdb=" O PHE E 81 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG E 79 " --> pdb=" O SER E 104 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 106 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR E 77 " --> pdb=" O ALA E 106 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF8, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AF9, first strand: chain 'E' and resid 220 through 221 removed outlier: 3.526A pdb=" N ARG E 220 " --> pdb=" O THR E 234 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 301 through 303 removed outlier: 3.872A pdb=" N ILE E 352 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY E 350 " --> pdb=" O TYR E 320 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 330 through 332 Processing sheet with id=AG3, first strand: chain 'E' and resid 337 through 339 Processing sheet with id=AG4, first strand: chain 'E' and resid 362 through 363 Processing sheet with id=AG5, first strand: chain 'E' and resid 387 through 388 removed outlier: 5.767A pdb=" N ARG F 295 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ILE F 315 " --> pdb=" O ARG F 295 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR F 297 " --> pdb=" O GLU F 313 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU F 313 " --> pdb=" O THR F 297 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 18 through 20 Processing sheet with id=AG7, first strand: chain 'F' and resid 35 through 39 removed outlier: 6.885A pdb=" N GLN F 50 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL F 38 " --> pdb=" O ARG F 48 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG F 48 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N SER F 52 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N MET F 71 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LYS F 67 " --> pdb=" O GLY F 56 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 35 through 39 removed outlier: 6.885A pdb=" N GLN F 50 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL F 38 " --> pdb=" O ARG F 48 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG F 48 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ILE F 49 " --> pdb=" O GLN F 108 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N GLN F 108 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 11.887A pdb=" N VAL F 51 " --> pdb=" O LEU F 106 " (cutoff:3.500A) removed outlier: 11.602A pdb=" N LEU F 106 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA F 53 " --> pdb=" O PHE F 104 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N PHE F 104 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR F 57 " --> pdb=" O HIS F 100 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N HIS F 100 " --> pdb=" O TYR F 57 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.614A pdb=" N SER F 114 " --> pdb=" O LYS F 132 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LYS F 132 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N THR F 116 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL F 130 " --> pdb=" O THR F 116 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 152 through 159 Processing sheet with id=AH2, first strand: chain 'F' and resid 241 through 242 removed outlier: 3.944A pdb=" N GLY F 257 " --> pdb=" O MET F 172 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 184 through 187 removed outlier: 4.659A pdb=" N VAL F 191 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR F 219 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 210 through 215 removed outlier: 3.608A pdb=" N GLY F 213 " --> pdb=" O TYR F 203 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL F 201 " --> pdb=" O VAL F 215 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 279 through 283 removed outlier: 3.655A pdb=" N THR F 279 " --> pdb=" O HIS F 290 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TRP F 283 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY F 286 " --> pdb=" O TRP F 283 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'T' and resid 3 through 6 683 hydrogen bonds defined for protein. 1827 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: 3.84 Time building geometry restraints manager: 2.18 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: 7161 1.34 - 1.47: 5755 1.47 - 1.60: 9545 1.60 - 1.73: 0 1.73 - 1.85: 162 Bond restraints: 22623 Sorted by residual: bond pdb=" C ARG A 157 " pdb=" N ASP A 158 " ideal model delta sigma weight residual 1.333 1.289 0.044 1.41e-02 5.03e+03 9.93e+00 bond pdb=" C ARG E 157 " pdb=" N ASP E 158 " ideal model delta sigma weight residual 1.333 1.289 0.044 1.41e-02 5.03e+03 9.71e+00 bond pdb=" C ARG C 157 " pdb=" N ASP C 158 " ideal model delta sigma weight residual 1.333 1.291 0.042 1.41e-02 5.03e+03 8.76e+00 bond pdb=" CB PHE D 73 " pdb=" CG PHE D 73 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.36e+00 bond pdb=" CB PHE F 73 " pdb=" CG PHE F 73 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.30e-02 1.89e+03 2.35e+00 ... (remaining 22618 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.54: 30778 5.54 - 11.07: 35 11.07 - 16.61: 0 16.61 - 22.15: 0 22.15 - 27.69: 9 Bond angle restraints: 30822 Sorted by residual: angle pdb=" N HIS F 75 " pdb=" CA HIS F 75 " pdb=" C HIS F 75 " ideal model delta sigma weight residual 111.37 139.06 -27.69 1.65e+00 3.67e-01 2.82e+02 angle pdb=" N HIS D 75 " pdb=" CA HIS D 75 " pdb=" C HIS D 75 " ideal model delta sigma weight residual 111.37 138.98 -27.61 1.65e+00 3.67e-01 2.80e+02 angle pdb=" N HIS B 75 " pdb=" CA HIS B 75 " pdb=" C HIS B 75 " ideal model delta sigma weight residual 111.37 138.96 -27.59 1.65e+00 3.67e-01 2.80e+02 angle pdb=" N ASP D 76 " pdb=" CA ASP D 76 " pdb=" CB ASP D 76 " ideal model delta sigma weight residual 110.71 136.16 -25.45 1.66e+00 3.63e-01 2.35e+02 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" CB ASP B 76 " ideal model delta sigma weight residual 110.71 136.11 -25.40 1.66e+00 3.63e-01 2.34e+02 ... (remaining 30817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12208 17.91 - 35.82: 1180 35.82 - 53.74: 177 53.74 - 71.65: 25 71.65 - 89.56: 21 Dihedral angle restraints: 13611 sinusoidal: 5310 harmonic: 8301 Sorted by residual: dihedral pdb=" N HIS D 75 " pdb=" C HIS D 75 " pdb=" CA HIS D 75 " pdb=" CB HIS D 75 " ideal model delta harmonic sigma weight residual 122.80 150.78 -27.98 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N HIS B 75 " pdb=" C HIS B 75 " pdb=" CA HIS B 75 " pdb=" CB HIS B 75 " ideal model delta harmonic sigma weight residual 122.80 150.76 -27.96 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N HIS F 75 " pdb=" C HIS F 75 " pdb=" CA HIS F 75 " pdb=" CB HIS F 75 " ideal model delta harmonic sigma weight residual 122.80 150.71 -27.91 0 2.50e+00 1.60e-01 1.25e+02 ... (remaining 13608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.291: 3504 0.291 - 0.582: 3 0.582 - 0.874: 0 0.874 - 1.165: 0 1.165 - 1.456: 3 Chirality restraints: 3510 Sorted by residual: chirality pdb=" CA HIS D 75 " pdb=" N HIS D 75 " pdb=" C HIS D 75 " pdb=" CB HIS D 75 " both_signs ideal model delta sigma weight residual False 2.51 1.05 1.46 2.00e-01 2.50e+01 5.30e+01 chirality pdb=" CA HIS B 75 " pdb=" N HIS B 75 " pdb=" C HIS B 75 " pdb=" CB HIS B 75 " both_signs ideal model delta sigma weight residual False 2.51 1.05 1.46 2.00e-01 2.50e+01 5.30e+01 chirality pdb=" CA HIS F 75 " pdb=" N HIS F 75 " pdb=" C HIS F 75 " pdb=" CB HIS F 75 " both_signs ideal model delta sigma weight residual False 2.51 1.06 1.45 2.00e-01 2.50e+01 5.29e+01 ... (remaining 3507 not shown) Planarity restraints: 3948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 266 " -0.038 5.00e-02 4.00e+02 5.71e-02 5.21e+00 pdb=" N PRO B 267 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 267 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 267 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 266 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO D 267 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 267 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 267 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 266 " -0.038 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO F 267 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO F 267 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 267 " -0.031 5.00e-02 4.00e+02 ... (remaining 3945 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3458 2.75 - 3.29: 19185 3.29 - 3.83: 31867 3.83 - 4.36: 35050 4.36 - 4.90: 64862 Nonbonded interactions: 154422 Sorted by model distance: nonbonded pdb=" O PRO F 368 " pdb=" OG1 THR F 371 " model vdw 2.216 3.040 nonbonded pdb=" O PRO D 368 " pdb=" OG1 THR D 371 " model vdw 2.218 3.040 nonbonded pdb=" O PRO B 368 " pdb=" OG1 THR B 371 " model vdw 2.218 3.040 nonbonded pdb=" O SER A 359 " pdb=" OG SER A 359 " model vdw 2.234 3.040 nonbonded pdb=" O SER E 359 " pdb=" OG SER E 359 " model vdw 2.234 3.040 ... (remaining 154417 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.080 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 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 : 0.008 0.051 22665 Z= 0.339 Angle : 0.931 27.686 30906 Z= 0.519 Chirality : 0.067 1.456 3510 Planarity : 0.007 0.057 3948 Dihedral : 13.856 89.561 8145 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.16 % Favored : 88.74 % Rotamer: Outliers : 0.37 % Allowed : 10.85 % Favored : 88.78 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.14 (0.13), residues: 2841 helix: -3.16 (0.22), residues: 282 sheet: -1.93 (0.15), residues: 912 loop : -3.29 (0.12), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 439 TYR 0.033 0.003 TYR C 308 PHE 0.032 0.003 PHE R 35 TRP 0.018 0.002 TRP D 39 HIS 0.015 0.002 HIS D 260 Details of bonding type rmsd covalent geometry : bond 0.00816 (22623) covalent geometry : angle 0.92528 (30822) SS BOND : bond 0.00941 ( 42) SS BOND : angle 2.14279 ( 84) hydrogen bonds : bond 0.32947 ( 653) hydrogen bonds : angle 8.76917 ( 1827) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 351 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.8601 (mtp) cc_final: 0.8373 (mtm) REVERT: A 307 ILE cc_start: 0.8480 (mt) cc_final: 0.8230 (pt) REVERT: A 362 GLN cc_start: 0.8006 (pt0) cc_final: 0.7782 (pm20) REVERT: A 364 ASN cc_start: 0.8022 (t0) cc_final: 0.7637 (t0) REVERT: B 84 MET cc_start: 0.9268 (mmm) cc_final: 0.8974 (mmt) REVERT: B 185 GLU cc_start: 0.7965 (tt0) cc_final: 0.7701 (tt0) REVERT: R 22 ASP cc_start: 0.8050 (m-30) cc_final: 0.7751 (m-30) REVERT: R 27 ILE cc_start: 0.8659 (mt) cc_final: 0.8451 (mm) REVERT: R 62 ASP cc_start: 0.8187 (t0) cc_final: 0.7826 (t70) REVERT: R 94 VAL cc_start: 0.9263 (t) cc_final: 0.7675 (m) REVERT: C 88 MET cc_start: 0.8565 (mtp) cc_final: 0.8318 (mtm) REVERT: D 84 MET cc_start: 0.9271 (mmm) cc_final: 0.8917 (mmt) REVERT: S 62 ASP cc_start: 0.8395 (t0) cc_final: 0.8015 (t0) REVERT: S 94 VAL cc_start: 0.9266 (t) cc_final: 0.8538 (m) REVERT: E 88 MET cc_start: 0.8665 (mtp) cc_final: 0.8464 (mtm) REVERT: T 22 ASP cc_start: 0.8126 (m-30) cc_final: 0.7728 (m-30) REVERT: T 33 ARG cc_start: 0.8808 (mmm-85) cc_final: 0.8524 (mmm160) REVERT: T 36 GLN cc_start: 0.8103 (tp-100) cc_final: 0.7894 (tt0) REVERT: T 91 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8085 (mt-10) outliers start: 9 outliers final: 4 residues processed: 358 average time/residue: 0.5977 time to fit residues: 243.7602 Evaluate side-chains 266 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 262 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 382 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 333 HIS B 161 HIS B 243 ASN B 322 ASN B 353 HIS R 3 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 333 HIS D 161 HIS D 243 ASN D 322 ASN E 327 HIS E 333 HIS E 362 GLN F 161 HIS F 243 ASN F 322 ASN F 336 ASN F 353 HIS F 365 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.065498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.052548 restraints weight = 58560.513| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 2.22 r_work: 0.2620 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22665 Z= 0.141 Angle : 0.706 11.119 30906 Z= 0.369 Chirality : 0.047 0.202 3510 Planarity : 0.006 0.049 3948 Dihedral : 5.958 51.845 3080 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.77 % Allowed : 14.73 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.14), residues: 2841 helix: -1.19 (0.27), residues: 330 sheet: -1.05 (0.16), residues: 927 loop : -2.73 (0.13), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 307 TYR 0.022 0.002 TYR D 404 PHE 0.014 0.001 PHE F 73 TRP 0.014 0.001 TRP B 334 HIS 0.008 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00304 (22623) covalent geometry : angle 0.70368 (30822) SS BOND : bond 0.00517 ( 42) SS BOND : angle 1.36232 ( 84) hydrogen bonds : bond 0.05958 ( 653) hydrogen bonds : angle 5.42507 ( 1827) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 297 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 PHE cc_start: 0.8151 (t80) cc_final: 0.7850 (t80) REVERT: A 19 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8367 (t) REVERT: A 303 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8386 (t) REVERT: B 85 GLU cc_start: 0.9361 (OUTLIER) cc_final: 0.8835 (mp0) REVERT: B 220 LYS cc_start: 0.9178 (ttpp) cc_final: 0.8967 (ttpp) REVERT: B 392 CYS cc_start: 0.7981 (t) cc_final: 0.7415 (p) REVERT: R 62 ASP cc_start: 0.8730 (t0) cc_final: 0.8362 (t0) REVERT: C 396 GLN cc_start: 0.8825 (tt0) cc_final: 0.8479 (tt0) REVERT: D 84 MET cc_start: 0.9276 (mmm) cc_final: 0.8945 (mmm) REVERT: S 62 ASP cc_start: 0.8687 (t0) cc_final: 0.8085 (t0) REVERT: S 94 VAL cc_start: 0.8545 (t) cc_final: 0.8099 (m) REVERT: E 289 ARG cc_start: 0.8638 (ptp-110) cc_final: 0.8034 (mtp-110) REVERT: E 303 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8529 (t) REVERT: E 321 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8068 (mtpp) REVERT: F 77 HIS cc_start: 0.6563 (OUTLIER) cc_final: 0.6274 (p90) REVERT: F 85 GLU cc_start: 0.9298 (OUTLIER) cc_final: 0.8456 (mp0) REVERT: T 47 ASP cc_start: 0.8268 (m-30) cc_final: 0.8021 (m-30) REVERT: T 91 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8501 (mt-10) outliers start: 68 outliers final: 24 residues processed: 337 average time/residue: 0.5670 time to fit residues: 218.9059 Evaluate side-chains 286 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 256 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain T residue 43 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 4 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 202 optimal weight: 0.0770 chunk 197 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 322 ASN R 3 HIS R 12 HIS R 76 HIS C 93 GLN C 319 GLN C 327 HIS C 362 GLN D 243 ASN D 322 ASN E 93 GLN E 319 GLN E 327 HIS E 362 GLN F 365 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.061973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.049041 restraints weight = 58975.043| |-----------------------------------------------------------------------------| r_work (start): 0.2598 rms_B_bonded: 2.24 r_work: 0.2520 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22665 Z= 0.179 Angle : 0.740 9.916 30906 Z= 0.387 Chirality : 0.048 0.175 3510 Planarity : 0.006 0.049 3948 Dihedral : 6.047 53.294 3080 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.57 % Allowed : 15.79 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.14), residues: 2841 helix: -0.66 (0.28), residues: 321 sheet: -0.61 (0.16), residues: 972 loop : -2.49 (0.13), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 324 TYR 0.036 0.002 TYR D 404 PHE 0.016 0.002 PHE D 73 TRP 0.015 0.002 TRP B 334 HIS 0.007 0.002 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00420 (22623) covalent geometry : angle 0.73667 (30822) SS BOND : bond 0.00638 ( 42) SS BOND : angle 1.56761 ( 84) hydrogen bonds : bond 0.06214 ( 653) hydrogen bonds : angle 5.13980 ( 1827) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 269 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 295 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8700 (p) REVERT: B 59 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8766 (tm-30) REVERT: B 398 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7485 (ttp80) REVERT: R 62 ASP cc_start: 0.8751 (t0) cc_final: 0.8337 (t0) REVERT: D 59 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: D 84 MET cc_start: 0.9164 (mmm) cc_final: 0.8880 (mmm) REVERT: S 22 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8713 (t70) REVERT: S 62 ASP cc_start: 0.8716 (t0) cc_final: 0.8456 (t70) REVERT: E 289 ARG cc_start: 0.8580 (ptp-110) cc_final: 0.8199 (mtp-110) REVERT: F 77 HIS cc_start: 0.6751 (OUTLIER) cc_final: 0.6204 (p90) REVERT: F 85 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: F 220 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8527 (ttmm) REVERT: F 283 TRP cc_start: 0.9312 (OUTLIER) cc_final: 0.7732 (p-90) REVERT: T 63 ARG cc_start: 0.8439 (ttm110) cc_final: 0.8132 (ttm-80) REVERT: T 91 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8443 (mt-10) outliers start: 112 outliers final: 39 residues processed: 355 average time/residue: 0.5489 time to fit residues: 225.7490 Evaluate side-chains 294 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 398 ARG Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 421 ILE Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain T residue 43 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 185 optimal weight: 0.9980 chunk 182 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 238 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 ASN R 3 HIS R 76 HIS C 327 HIS D 243 ASN D 322 ASN E 327 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.063463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.050587 restraints weight = 58393.787| |-----------------------------------------------------------------------------| r_work (start): 0.2630 rms_B_bonded: 2.15 r_work: 0.2554 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2463 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22665 Z= 0.145 Angle : 0.680 9.723 30906 Z= 0.354 Chirality : 0.046 0.153 3510 Planarity : 0.006 0.044 3948 Dihedral : 5.748 52.141 3078 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 4.00 % Allowed : 17.34 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.15), residues: 2841 helix: -0.35 (0.28), residues: 321 sheet: -0.31 (0.16), residues: 999 loop : -2.36 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 324 TYR 0.036 0.002 TYR D 404 PHE 0.011 0.001 PHE D 73 TRP 0.013 0.001 TRP B 334 HIS 0.009 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00331 (22623) covalent geometry : angle 0.67681 (30822) SS BOND : bond 0.00501 ( 42) SS BOND : angle 1.34913 ( 84) hydrogen bonds : bond 0.05164 ( 653) hydrogen bonds : angle 4.89009 ( 1827) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 265 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.8850 (mp0) REVERT: B 145 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8828 (mp) REVERT: B 283 TRP cc_start: 0.9457 (OUTLIER) cc_final: 0.8056 (p-90) REVERT: B 404 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.8327 (t80) REVERT: R 56 TYR cc_start: 0.6845 (m-10) cc_final: 0.6605 (m-10) REVERT: C 144 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8727 (pp) REVERT: D 59 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8861 (tt0) REVERT: D 84 MET cc_start: 0.9163 (mmm) cc_final: 0.8908 (mmm) REVERT: D 85 GLU cc_start: 0.9462 (OUTLIER) cc_final: 0.8733 (mt-10) REVERT: S 62 ASP cc_start: 0.8801 (t0) cc_final: 0.8378 (t0) REVERT: E 289 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8200 (mtp-110) REVERT: F 77 HIS cc_start: 0.6849 (OUTLIER) cc_final: 0.6288 (p90) REVERT: F 85 GLU cc_start: 0.9350 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: F 220 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8693 (ttmm) REVERT: F 283 TRP cc_start: 0.9308 (OUTLIER) cc_final: 0.7758 (p-90) REVERT: F 401 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7088 (tm) outliers start: 98 outliers final: 44 residues processed: 334 average time/residue: 0.5661 time to fit residues: 217.5004 Evaluate side-chains 305 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 250 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 283 TRP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 404 TYR Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain T residue 25 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 255 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 223 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 236 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 322 ASN R 3 HIS R 12 HIS R 76 HIS ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 ASN D 322 ASN E 319 GLN E 327 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.061075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.048414 restraints weight = 58110.733| |-----------------------------------------------------------------------------| r_work (start): 0.2570 rms_B_bonded: 2.11 r_work: 0.2492 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22665 Z= 0.206 Angle : 0.782 9.620 30906 Z= 0.407 Chirality : 0.049 0.172 3510 Planarity : 0.006 0.049 3948 Dihedral : 6.109 51.700 3078 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.04 % Allowed : 18.56 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.14), residues: 2841 helix: -0.45 (0.27), residues: 324 sheet: -0.23 (0.17), residues: 915 loop : -2.35 (0.13), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 398 TYR 0.037 0.002 TYR D 404 PHE 0.016 0.002 PHE C 51 TRP 0.015 0.002 TRP B 334 HIS 0.008 0.002 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00491 (22623) covalent geometry : angle 0.77859 (30822) SS BOND : bond 0.00671 ( 42) SS BOND : angle 1.66116 ( 84) hydrogen bonds : bond 0.06114 ( 653) hydrogen bonds : angle 5.02452 ( 1827) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 268 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 418 SER cc_start: 0.8556 (p) cc_final: 0.8254 (t) REVERT: B 145 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.8855 (mp) REVERT: B 283 TRP cc_start: 0.9469 (OUTLIER) cc_final: 0.8205 (p-90) REVERT: R 60 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8409 (mptt) REVERT: D 59 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8831 (tt0) REVERT: D 84 MET cc_start: 0.9169 (mmm) cc_final: 0.8878 (mmm) REVERT: S 62 ASP cc_start: 0.8808 (t0) cc_final: 0.8466 (t0) REVERT: E 289 ARG cc_start: 0.8611 (ptp-110) cc_final: 0.8120 (mtp-110) REVERT: F 77 HIS cc_start: 0.6825 (OUTLIER) cc_final: 0.6085 (p90) REVERT: F 85 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: F 283 TRP cc_start: 0.9319 (OUTLIER) cc_final: 0.7787 (p-90) REVERT: T 62 ASP cc_start: 0.8419 (t0) cc_final: 0.7922 (p0) REVERT: T 63 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7489 (ttm-80) outliers start: 99 outliers final: 54 residues processed: 340 average time/residue: 0.5220 time to fit residues: 205.0576 Evaluate side-chains 317 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 283 TRP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 209 ASP Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain F residue 294 MET Chi-restraints excluded: chain T residue 25 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 229 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 0.3980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 322 ASN R 3 HIS R 12 HIS R 76 HIS C 327 HIS D 243 ASN D 322 ASN S 12 HIS E 319 GLN F 357 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.061902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.049082 restraints weight = 58841.236| |-----------------------------------------------------------------------------| r_work (start): 0.2582 rms_B_bonded: 2.23 r_work: 0.2503 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22665 Z= 0.160 Angle : 0.729 10.549 30906 Z= 0.376 Chirality : 0.046 0.161 3510 Planarity : 0.006 0.046 3948 Dihedral : 5.873 51.368 3078 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.43 % Allowed : 19.99 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.15), residues: 2841 helix: -0.25 (0.27), residues: 324 sheet: -0.16 (0.17), residues: 972 loop : -2.34 (0.14), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 324 TYR 0.036 0.002 TYR D 404 PHE 0.012 0.002 PHE A 170 TRP 0.013 0.001 TRP B 334 HIS 0.010 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00372 (22623) covalent geometry : angle 0.72496 (30822) SS BOND : bond 0.00492 ( 42) SS BOND : angle 1.64714 ( 84) hydrogen bonds : bond 0.05305 ( 653) hydrogen bonds : angle 4.86444 ( 1827) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 269 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 SER cc_start: 0.8471 (p) cc_final: 0.8192 (t) REVERT: B 85 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.8844 (mp0) REVERT: B 283 TRP cc_start: 0.9423 (OUTLIER) cc_final: 0.8051 (p-90) REVERT: C 144 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8733 (pp) REVERT: D 59 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8886 (tt0) REVERT: D 84 MET cc_start: 0.9165 (mmm) cc_final: 0.8909 (mmm) REVERT: D 85 GLU cc_start: 0.9473 (OUTLIER) cc_final: 0.8705 (mt-10) REVERT: D 185 GLU cc_start: 0.8461 (tt0) cc_final: 0.8092 (tt0) REVERT: D 221 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7580 (mpp) REVERT: S 62 ASP cc_start: 0.8754 (t0) cc_final: 0.8343 (t70) REVERT: E 212 ASP cc_start: 0.8289 (p0) cc_final: 0.8018 (p0) REVERT: E 289 ARG cc_start: 0.8582 (ptp-110) cc_final: 0.8056 (mtp-110) REVERT: F 77 HIS cc_start: 0.6747 (OUTLIER) cc_final: 0.5928 (p90) REVERT: F 85 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: F 220 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8477 (ttmm) REVERT: F 283 TRP cc_start: 0.9268 (OUTLIER) cc_final: 0.7669 (p-90) REVERT: T 62 ASP cc_start: 0.8431 (t0) cc_final: 0.7910 (p0) outliers start: 84 outliers final: 51 residues processed: 329 average time/residue: 0.5563 time to fit residues: 211.7616 Evaluate side-chains 319 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 258 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 283 TRP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 383 LEU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 321 LYS Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 241 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 322 ASN B 357 HIS R 3 HIS R 12 HIS C 100 ASN C 327 HIS D 243 ASN D 322 ASN S 12 HIS E 100 ASN E 319 GLN F 357 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.050664 restraints weight = 58533.756| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.24 r_work: 0.2547 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22665 Z= 0.130 Angle : 0.676 10.967 30906 Z= 0.346 Chirality : 0.045 0.163 3510 Planarity : 0.005 0.046 3948 Dihedral : 5.475 50.020 3078 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.35 % Allowed : 20.48 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.15), residues: 2841 helix: 0.01 (0.28), residues: 324 sheet: 0.24 (0.17), residues: 936 loop : -2.29 (0.14), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 324 TYR 0.032 0.001 TYR D 404 PHE 0.010 0.001 PHE A 170 TRP 0.011 0.001 TRP B 334 HIS 0.010 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00294 (22623) covalent geometry : angle 0.67303 (30822) SS BOND : bond 0.00396 ( 42) SS BOND : angle 1.35826 ( 84) hydrogen bonds : bond 0.04540 ( 653) hydrogen bonds : angle 4.64338 ( 1827) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 269 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 234 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8657 (t) REVERT: B 85 GLU cc_start: 0.9391 (OUTLIER) cc_final: 0.8849 (mp0) REVERT: B 283 TRP cc_start: 0.9397 (OUTLIER) cc_final: 0.8025 (p-90) REVERT: R 12 HIS cc_start: 0.8037 (t70) cc_final: 0.7821 (t-90) REVERT: C 376 CYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7338 (m) REVERT: D 59 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: D 84 MET cc_start: 0.9137 (mmm) cc_final: 0.8903 (mmm) REVERT: D 85 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.8722 (mt-10) REVERT: S 4 TYR cc_start: 0.8576 (m-80) cc_final: 0.8266 (m-80) REVERT: S 47 ASP cc_start: 0.8113 (m-30) cc_final: 0.7909 (m-30) REVERT: S 62 ASP cc_start: 0.8721 (t0) cc_final: 0.8387 (t70) REVERT: E 212 ASP cc_start: 0.8254 (p0) cc_final: 0.8021 (p0) REVERT: E 289 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7962 (mtp-110) REVERT: F 77 HIS cc_start: 0.6334 (OUTLIER) cc_final: 0.5783 (p90) REVERT: F 85 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: F 283 TRP cc_start: 0.9238 (OUTLIER) cc_final: 0.7591 (p-90) REVERT: T 62 ASP cc_start: 0.8441 (t0) cc_final: 0.7906 (p0) REVERT: T 63 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8012 (ttm110) outliers start: 82 outliers final: 41 residues processed: 329 average time/residue: 0.5543 time to fit residues: 211.0314 Evaluate side-chains 307 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 283 TRP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain T residue 25 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 86 optimal weight: 9.9990 chunk 216 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 261 optimal weight: 0.9980 chunk 139 optimal weight: 8.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN R 3 HIS R 76 HIS C 319 GLN D 243 ASN D 322 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.062241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.049405 restraints weight = 58381.529| |-----------------------------------------------------------------------------| r_work (start): 0.2590 rms_B_bonded: 2.23 r_work: 0.2513 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22665 Z= 0.158 Angle : 0.736 12.609 30906 Z= 0.377 Chirality : 0.046 0.195 3510 Planarity : 0.006 0.054 3948 Dihedral : 5.667 48.596 3078 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.02 % Allowed : 21.05 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.15), residues: 2841 helix: -0.05 (0.27), residues: 324 sheet: 0.11 (0.17), residues: 939 loop : -2.26 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 324 TYR 0.034 0.002 TYR D 404 PHE 0.011 0.002 PHE A 170 TRP 0.013 0.001 TRP B 334 HIS 0.006 0.001 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00370 (22623) covalent geometry : angle 0.73220 (30822) SS BOND : bond 0.00484 ( 42) SS BOND : angle 1.58415 ( 84) hydrogen bonds : bond 0.05038 ( 653) hydrogen bonds : angle 4.71669 ( 1827) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 264 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8686 (t) REVERT: B 85 GLU cc_start: 0.9410 (OUTLIER) cc_final: 0.8871 (mp0) REVERT: B 145 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8791 (mp) REVERT: B 283 TRP cc_start: 0.9421 (OUTLIER) cc_final: 0.8074 (p-90) REVERT: R 12 HIS cc_start: 0.8147 (t70) cc_final: 0.7931 (t-90) REVERT: R 22 ASP cc_start: 0.8972 (m-30) cc_final: 0.8740 (m-30) REVERT: C 376 CYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7357 (m) REVERT: D 59 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8891 (tt0) REVERT: D 84 MET cc_start: 0.9153 (mmm) cc_final: 0.8907 (mmm) REVERT: D 221 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.7503 (mpp) REVERT: S 62 ASP cc_start: 0.8677 (t0) cc_final: 0.8405 (t70) REVERT: E 289 ARG cc_start: 0.8493 (ptp-110) cc_final: 0.8018 (mtp-110) REVERT: F 77 HIS cc_start: 0.6545 (OUTLIER) cc_final: 0.5817 (p90) REVERT: F 85 GLU cc_start: 0.9360 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: F 283 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.7658 (p-90) REVERT: T 62 ASP cc_start: 0.8502 (t0) cc_final: 0.7977 (p0) outliers start: 74 outliers final: 48 residues processed: 319 average time/residue: 0.5322 time to fit residues: 196.8148 Evaluate side-chains 316 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 283 TRP Chi-restraints excluded: chain B residue 294 MET Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain E residue 426 ILE Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 242 optimal weight: 0.0370 chunk 68 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.5264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN R 3 HIS R 76 HIS D 243 ASN D 322 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.062831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.049947 restraints weight = 58493.866| |-----------------------------------------------------------------------------| r_work (start): 0.2604 rms_B_bonded: 2.23 r_work: 0.2526 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22665 Z= 0.147 Angle : 0.724 12.656 30906 Z= 0.370 Chirality : 0.046 0.183 3510 Planarity : 0.006 0.052 3948 Dihedral : 5.561 47.432 3078 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.06 % Allowed : 21.01 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.15), residues: 2841 helix: 0.06 (0.27), residues: 324 sheet: 0.18 (0.17), residues: 966 loop : -2.25 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 324 TYR 0.040 0.002 TYR D 404 PHE 0.010 0.001 PHE A 170 TRP 0.012 0.001 TRP B 334 HIS 0.006 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00342 (22623) covalent geometry : angle 0.72087 (30822) SS BOND : bond 0.00448 ( 42) SS BOND : angle 1.49935 ( 84) hydrogen bonds : bond 0.04794 ( 653) hydrogen bonds : angle 4.65934 ( 1827) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 267 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 234 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8688 (t) REVERT: B 85 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.8863 (mp0) REVERT: B 145 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8764 (mp) REVERT: B 283 TRP cc_start: 0.9410 (OUTLIER) cc_final: 0.8059 (p-90) REVERT: R 8 GLU cc_start: 0.7790 (tp30) cc_final: 0.7557 (tp30) REVERT: R 9 GLU cc_start: 0.8082 (tp30) cc_final: 0.7729 (tp30) REVERT: R 62 ASP cc_start: 0.8715 (t0) cc_final: 0.8419 (t0) REVERT: C 376 CYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7358 (m) REVERT: D 59 GLN cc_start: 0.9191 (OUTLIER) cc_final: 0.8903 (tt0) REVERT: D 84 MET cc_start: 0.9143 (mmm) cc_final: 0.8910 (mmm) REVERT: D 85 GLU cc_start: 0.9469 (OUTLIER) cc_final: 0.8712 (mt-10) REVERT: D 221 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7412 (mpp) REVERT: S 4 TYR cc_start: 0.8640 (m-80) cc_final: 0.8309 (m-80) REVERT: S 9 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7264 (tp30) REVERT: S 62 ASP cc_start: 0.8678 (t0) cc_final: 0.8370 (t70) REVERT: E 212 ASP cc_start: 0.8226 (p0) cc_final: 0.7947 (p0) REVERT: E 289 ARG cc_start: 0.8459 (ptp-110) cc_final: 0.8061 (mtp-110) REVERT: F 77 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.5800 (p90) REVERT: F 85 GLU cc_start: 0.9356 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: F 283 TRP cc_start: 0.9257 (OUTLIER) cc_final: 0.7624 (p-90) REVERT: T 9 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7320 (tp30) REVERT: T 62 ASP cc_start: 0.8477 (t0) cc_final: 0.7953 (p0) outliers start: 75 outliers final: 46 residues processed: 323 average time/residue: 0.5848 time to fit residues: 218.2471 Evaluate side-chains 318 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 261 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 283 TRP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 300 SER Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 373 LYS Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 268 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN R 3 HIS R 76 HIS C 100 ASN C 270 ASN C 319 GLN C 399 GLN D 243 ASN D 322 ASN E 327 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.058778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.046212 restraints weight = 58745.820| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 2.20 r_work: 0.2423 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2329 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 22665 Z= 0.282 Angle : 0.910 13.472 30906 Z= 0.473 Chirality : 0.052 0.243 3510 Planarity : 0.007 0.055 3948 Dihedral : 6.424 45.939 3078 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.90 % Allowed : 21.46 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.14), residues: 2841 helix: -0.38 (0.26), residues: 324 sheet: 0.14 (0.17), residues: 903 loop : -2.43 (0.13), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 324 TYR 0.037 0.003 TYR D 404 PHE 0.025 0.003 PHE B 73 TRP 0.017 0.002 TRP F 283 HIS 0.010 0.002 HIS C 355 Details of bonding type rmsd covalent geometry : bond 0.00694 (22623) covalent geometry : angle 0.90415 (30822) SS BOND : bond 0.00816 ( 42) SS BOND : angle 2.17850 ( 84) hydrogen bonds : bond 0.06827 ( 653) hydrogen bonds : angle 5.10846 ( 1827) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 265 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 234 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8713 (t) REVERT: B 145 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.8788 (mp) REVERT: B 283 TRP cc_start: 0.9438 (OUTLIER) cc_final: 0.8104 (p-90) REVERT: R 9 GLU cc_start: 0.8282 (tp30) cc_final: 0.7699 (tp30) REVERT: R 62 ASP cc_start: 0.8746 (t0) cc_final: 0.8329 (t70) REVERT: D 59 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8940 (tt0) REVERT: D 84 MET cc_start: 0.9196 (mmm) cc_final: 0.8894 (mmm) REVERT: D 85 GLU cc_start: 0.9460 (OUTLIER) cc_final: 0.8629 (mt-10) REVERT: D 221 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7578 (mpp) REVERT: S 62 ASP cc_start: 0.8670 (t0) cc_final: 0.8389 (t70) REVERT: S 83 ASN cc_start: 0.9015 (t0) cc_final: 0.8776 (t0) REVERT: E 212 ASP cc_start: 0.8222 (p0) cc_final: 0.7953 (p0) REVERT: E 289 ARG cc_start: 0.8570 (ptp-110) cc_final: 0.8165 (mtp-110) REVERT: F 77 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.5886 (p90) REVERT: F 85 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: F 220 LYS cc_start: 0.9279 (ttpp) cc_final: 0.8920 (ttpp) REVERT: F 283 TRP cc_start: 0.9298 (OUTLIER) cc_final: 0.7809 (p-90) REVERT: T 9 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7065 (tp30) REVERT: T 11 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7484 (mm-30) REVERT: T 62 ASP cc_start: 0.8490 (t0) cc_final: 0.8044 (p0) outliers start: 71 outliers final: 50 residues processed: 327 average time/residue: 0.5747 time to fit residues: 217.5529 Evaluate side-chains 312 residues out of total 2451 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 253 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 374 SER Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 75 HIS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 283 TRP Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 402 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain C residue 125 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 319 GLN Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 379 GLU Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 59 GLN Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 75 HIS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 221 MET Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 283 TRP Chi-restraints excluded: chain D residue 300 THR Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 52 THR Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain E residue 219 ILE Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 376 CYS Chi-restraints excluded: chain F residue 23 CYS Chi-restraints excluded: chain F residue 75 HIS Chi-restraints excluded: chain F residue 77 HIS Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain F residue 139 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 277 THR Chi-restraints excluded: chain F residue 283 TRP Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 240 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 161 optimal weight: 4.9990 chunk 216 optimal weight: 0.0570 chunk 248 optimal weight: 0.4980 chunk 0 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 319 GLN B 322 ASN R 3 HIS R 76 HIS R 83 ASN C 100 ASN C 319 GLN D 243 ASN D 322 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.063520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.050759 restraints weight = 58514.350| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 2.24 r_work: 0.2548 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2455 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22665 Z= 0.132 Angle : 0.718 13.139 30906 Z= 0.366 Chirality : 0.045 0.161 3510 Planarity : 0.006 0.061 3948 Dihedral : 5.563 46.036 3078 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.20 % Allowed : 22.85 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.15), residues: 2841 helix: 0.18 (0.28), residues: 324 sheet: 0.32 (0.17), residues: 903 loop : -2.26 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 324 TYR 0.033 0.001 TYR D 404 PHE 0.010 0.001 PHE E 95 TRP 0.009 0.001 TRP B 334 HIS 0.005 0.001 HIS D 357 Details of bonding type rmsd covalent geometry : bond 0.00299 (22623) covalent geometry : angle 0.71483 (30822) SS BOND : bond 0.00341 ( 42) SS BOND : angle 1.49361 ( 84) hydrogen bonds : bond 0.04572 ( 653) hydrogen bonds : angle 4.73072 ( 1827) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8341.49 seconds wall clock time: 142 minutes 31.08 seconds (8551.08 seconds total)