Starting phenix.real_space_refine on Sun Feb 8 07:21:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n8x_49152/02_2026/9n8x_49152.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n8x_49152/02_2026/9n8x_49152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n8x_49152/02_2026/9n8x_49152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n8x_49152/02_2026/9n8x_49152.map" model { file = "/net/cci-nas-00/data/ceres_data/9n8x_49152/02_2026/9n8x_49152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n8x_49152/02_2026/9n8x_49152.cif" } resolution = 3.5 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= 0.004 sd= 0.046 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1 5.49 5 S 102 5.16 5 C 26461 2.51 5 N 7110 2.21 5 O 7867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 41543 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3123 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 16, 'TRANS': 375} Chain: "B" Number of atoms: 6491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6491 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 45, 'TRANS': 805} Chain breaks: 1 Chain: "C" Number of atoms: 6486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6486 Classifications: {'peptide': 850} Link IDs: {'PTRANS': 45, 'TRANS': 804} Chain breaks: 1 Chain: "D" Number of atoms: 6378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6378 Classifications: {'peptide': 847} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 44, 'TRANS': 802} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'TRP:plan': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6273 Classifications: {'peptide': 826} Link IDs: {'PTRANS': 43, 'TRANS': 782} Chain breaks: 1 Chain: "F" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6273 Classifications: {'peptide': 826} Link IDs: {'PTRANS': 43, 'TRANS': 782} Chain breaks: 1 Chain: "G" Number of atoms: 6478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 849, 6478 Classifications: {'peptide': 849} Link IDs: {'PTRANS': 44, 'TRANS': 804} Chain breaks: 1 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' ZN': 2, 'PEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 46 SG CYS A 31 58.009 51.831 23.067 1.00149.64 S ATOM 68 SG CYS A 34 56.360 48.822 21.665 1.00154.47 S ATOM 203 SG CYS A 51 54.579 52.136 21.454 1.00170.93 S ATOM 227 SG CYS A 54 54.907 50.494 24.823 1.00171.65 S ATOM 1662 SG CYS A 233 72.178 55.180 24.765 1.00141.66 S ATOM 1680 SG CYS A 236 71.281 58.723 24.324 1.00142.51 S ATOM 1780 SG CYS A 248 74.066 57.305 22.141 1.00171.98 S ATOM 1804 SG CYS A 251 74.604 57.783 25.848 1.00167.17 S Time building chain proxies: 9.08, per 1000 atoms: 0.22 Number of scatterers: 41543 At special positions: 0 Unit cell: (114.756, 112.59, 311.789, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 102 16.00 P 1 15.00 O 7867 8.00 N 7110 7.00 C 26461 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 34 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 51 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 54 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 31 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 251 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 233 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 236 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 248 " Number of angles added : 12 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9826 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 64 sheets defined 17.8% alpha, 31.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 65 through 85 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.764A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.536A pdb=" N LEU A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 189 through 206 removed outlier: 4.300A pdb=" N SER A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 218 removed outlier: 3.957A pdb=" N LEU A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 283 removed outlier: 4.031A pdb=" N LEU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 298 through 322 removed outlier: 3.796A pdb=" N ILE A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.673A pdb=" N PHE A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 361 removed outlier: 3.871A pdb=" N ILE A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.568A pdb=" N PHE A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 409 Processing helix chain 'A' and resid 410 through 417 removed outlier: 4.178A pdb=" N LEU A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 418 No H-bonds generated for 'chain 'A' and resid 418 through 418' Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.599A pdb=" N ILE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 4.227A pdb=" N ASP B 100 " --> pdb=" O ASP B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 209 through 215 removed outlier: 5.088A pdb=" N ASP B 213 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 215 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.897A pdb=" N LEU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 335 removed outlier: 3.757A pdb=" N VAL B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR B 333 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.574A pdb=" N GLY B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.551A pdb=" N GLU B 389 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 445 removed outlier: 4.707A pdb=" N GLU B 443 " --> pdb=" O GLN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 507 Processing helix chain 'B' and resid 560 through 567 removed outlier: 4.849A pdb=" N ASN B 565 " --> pdb=" O GLU B 562 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 601 Processing helix chain 'B' and resid 626 through 632 Processing helix chain 'B' and resid 711 through 715 removed outlier: 3.804A pdb=" N LEU B 715 " --> pdb=" O ASP B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 Processing helix chain 'B' and resid 830 through 834 Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 24 through 45 removed outlier: 4.435A pdb=" N PHE C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 4.246A pdb=" N ASP C 100 " --> pdb=" O ASP C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 209 through 215 removed outlier: 5.083A pdb=" N ASP C 213 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 215 " --> pdb=" O THR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.755A pdb=" N VAL C 332 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR C 333 " --> pdb=" O SER C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.573A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.543A pdb=" N GLU C 389 " --> pdb=" O LEU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 445 removed outlier: 4.716A pdb=" N GLU C 443 " --> pdb=" O GLN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 560 through 567 removed outlier: 4.812A pdb=" N ASN C 565 " --> pdb=" O GLU C 562 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU C 567 " --> pdb=" O ARG C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'C' and resid 626 through 632 Processing helix chain 'C' and resid 711 through 715 removed outlier: 3.804A pdb=" N LEU C 715 " --> pdb=" O ASP C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 Processing helix chain 'C' and resid 830 through 834 Processing helix chain 'D' and resid 26 through 44 removed outlier: 4.012A pdb=" N ASP D 44 " --> pdb=" O ASP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 4.246A pdb=" N ASP D 100 " --> pdb=" O ASP D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 209 through 215 removed outlier: 5.083A pdb=" N ASP D 213 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 215 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.892A pdb=" N LEU D 246 " --> pdb=" O SER D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 335 removed outlier: 3.753A pdb=" N VAL D 332 " --> pdb=" O PRO D 329 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR D 333 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.598A pdb=" N GLY D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 389 removed outlier: 3.528A pdb=" N GLU D 389 " --> pdb=" O LEU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 445 removed outlier: 4.718A pdb=" N GLU D 443 " --> pdb=" O GLN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 507 Processing helix chain 'D' and resid 560 through 567 removed outlier: 4.838A pdb=" N ASN D 565 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU D 567 " --> pdb=" O ARG D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 601 Processing helix chain 'D' and resid 626 through 632 Processing helix chain 'D' and resid 711 through 715 removed outlier: 3.811A pdb=" N LEU D 715 " --> pdb=" O ASP D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 802 Processing helix chain 'D' and resid 830 through 834 Processing helix chain 'E' and resid 97 through 101 removed outlier: 4.230A pdb=" N ASP E 100 " --> pdb=" O ASP E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 129 Processing helix chain 'E' and resid 209 through 215 removed outlier: 5.086A pdb=" N ASP E 213 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL E 215 " --> pdb=" O THR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 248 Processing helix chain 'E' and resid 329 through 332 removed outlier: 3.764A pdb=" N VAL E 332 " --> pdb=" O PRO E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 332' Processing helix chain 'E' and resid 354 through 361 removed outlier: 3.596A pdb=" N GLY E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 389 removed outlier: 3.511A pdb=" N GLU E 389 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 445 removed outlier: 4.708A pdb=" N GLU E 443 " --> pdb=" O GLN E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 507 Processing helix chain 'E' and resid 560 through 567 removed outlier: 4.800A pdb=" N ASN E 565 " --> pdb=" O GLU E 562 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU E 567 " --> pdb=" O ARG E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 Processing helix chain 'E' and resid 626 through 632 Processing helix chain 'E' and resid 798 through 802 Processing helix chain 'E' and resid 830 through 834 Processing helix chain 'F' and resid 97 through 101 removed outlier: 4.237A pdb=" N ASP F 100 " --> pdb=" O ASP F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 209 through 215 removed outlier: 5.111A pdb=" N ASP F 213 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 215 " --> pdb=" O THR F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 248 removed outlier: 3.859A pdb=" N LEU F 246 " --> pdb=" O SER F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 335 removed outlier: 3.766A pdb=" N VAL F 332 " --> pdb=" O PRO F 329 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N THR F 333 " --> pdb=" O SER F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 361 removed outlier: 3.590A pdb=" N GLY F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 445 removed outlier: 4.726A pdb=" N GLU F 443 " --> pdb=" O GLN F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 500 through 507 Processing helix chain 'F' and resid 560 through 567 removed outlier: 4.830A pdb=" N ASN F 565 " --> pdb=" O GLU F 562 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU F 567 " --> pdb=" O ARG F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 601 Processing helix chain 'F' and resid 626 through 632 Processing helix chain 'F' and resid 711 through 715 removed outlier: 3.812A pdb=" N LEU F 715 " --> pdb=" O ASP F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 830 through 834 Processing helix chain 'F' and resid 867 through 871 removed outlier: 3.521A pdb=" N TRP F 871 " --> pdb=" O TRP F 868 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 44 removed outlier: 3.524A pdb=" N PHE G 28 " --> pdb=" O TRP G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 4.218A pdb=" N ASP G 100 " --> pdb=" O ASP G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 129 Processing helix chain 'G' and resid 209 through 215 removed outlier: 5.100A pdb=" N ASP G 213 " --> pdb=" O ARG G 210 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL G 215 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 248 Processing helix chain 'G' and resid 329 through 335 removed outlier: 3.755A pdb=" N VAL G 332 " --> pdb=" O PRO G 329 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N THR G 333 " --> pdb=" O SER G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 361 removed outlier: 3.573A pdb=" N GLY G 361 " --> pdb=" O ALA G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 445 removed outlier: 4.719A pdb=" N GLU G 443 " --> pdb=" O GLN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 479 Processing helix chain 'G' and resid 500 through 507 Processing helix chain 'G' and resid 560 through 567 removed outlier: 4.837A pdb=" N ASN G 565 " --> pdb=" O GLU G 562 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU G 567 " --> pdb=" O ARG G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 600 Processing helix chain 'G' and resid 626 through 632 Processing helix chain 'G' and resid 798 through 802 Processing helix chain 'G' and resid 830 through 834 Processing helix chain 'G' and resid 867 through 871 removed outlier: 3.522A pdb=" N TRP G 871 " --> pdb=" O TRP G 868 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 100 removed outlier: 4.066A pdb=" N ALA A 100 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 89 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 184 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 232 removed outlier: 3.870A pdb=" N ARG A 231 " --> pdb=" O GLY A 240 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 240 " --> pdb=" O ARG A 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 290 Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.549A pdb=" N MET B 134 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N VAL B 76 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N SER B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.203A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU B 178 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE B 253 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 180 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 250 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 227 through 230 Processing sheet with id=AA8, first strand: chain 'B' and resid 340 through 344 removed outlier: 3.568A pdb=" N LEU B 366 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 393 through 399 removed outlier: 6.266A pdb=" N ALA B 436 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL B 421 " --> pdb=" O ALA B 436 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 458 through 460 Processing sheet with id=AB2, first strand: chain 'B' and resid 517 through 521 removed outlier: 6.232A pdb=" N HIS B 558 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL B 543 " --> pdb=" O HIS B 558 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 532 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE B 605 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 534 " --> pdb=" O PHE B 605 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 580 through 584 Processing sheet with id=AB4, first strand: chain 'B' and resid 695 through 698 removed outlier: 6.735A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU B 668 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU B 674 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 749 through 754 removed outlier: 6.458A pdb=" N ARG B 793 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 776 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE B 840 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 816 through 818 removed outlier: 4.038A pdb=" N LEU B 816 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL C 825 " --> pdb=" O LEU B 816 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY C 823 " --> pdb=" O PHE B 818 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 822 through 825 removed outlier: 3.736A pdb=" N VAL B 825 " --> pdb=" O LEU G 816 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU G 816 " --> pdb=" O VAL B 825 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 107 through 111 removed outlier: 3.584A pdb=" N MET C 134 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.197A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 236 through 239 removed outlier: 3.799A pdb=" N VAL C 227 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL D 238 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 340 through 344 removed outlier: 3.573A pdb=" N LEU C 366 " --> pdb=" O MET C 301 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 393 through 399 removed outlier: 6.286A pdb=" N ALA C 436 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL C 421 " --> pdb=" O ALA C 436 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N PHE C 451 " --> pdb=" O TYR C 498 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 458 through 460 Processing sheet with id=AC5, first strand: chain 'C' and resid 517 through 521 removed outlier: 6.128A pdb=" N HIS C 558 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N VAL C 543 " --> pdb=" O HIS C 558 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE C 573 " --> pdb=" O TYR C 624 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 588 through 591 removed outlier: 3.557A pdb=" N LEU D 588 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 695 through 698 removed outlier: 3.505A pdb=" N VAL C 721 " --> pdb=" O ARG C 654 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU C 668 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLU C 674 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 749 through 754 removed outlier: 6.469A pdb=" N ARG C 793 " --> pdb=" O VAL C 776 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL C 776 " --> pdb=" O ARG C 793 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 840 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 816 through 819 removed outlier: 3.822A pdb=" N LEU C 816 " --> pdb=" O VAL D 825 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL D 825 " --> pdb=" O LEU C 816 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 107 through 111 removed outlier: 3.549A pdb=" N MET D 134 " --> pdb=" O ARG D 67 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL D 76 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N SER D 93 " --> pdb=" O VAL D 76 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.184A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU D 178 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N PHE D 253 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TYR D 180 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D 250 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N PHE D 268 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS D 164 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU D 270 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN D 166 " --> pdb=" O LEU D 270 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 340 through 344 removed outlier: 3.569A pdb=" N LEU D 366 " --> pdb=" O MET D 301 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 450 through 453 removed outlier: 6.489A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL D 421 " --> pdb=" O ALA D 436 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA D 436 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N TYR D 495 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR D 396 " --> pdb=" O TYR D 495 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AD6, first strand: chain 'D' and resid 517 through 521 removed outlier: 6.465A pdb=" N HIS D 558 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL D 543 " --> pdb=" O HIS D 558 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL D 532 " --> pdb=" O ILE D 603 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N PHE D 605 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LEU D 534 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 695 through 698 removed outlier: 6.754A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU D 668 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU D 674 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 749 through 754 removed outlier: 6.455A pdb=" N ARG D 793 " --> pdb=" O VAL D 776 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL D 776 " --> pdb=" O ARG D 793 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 840 " --> pdb=" O LEU D 767 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 815 through 818 removed outlier: 3.957A pdb=" N LEU D 816 " --> pdb=" O VAL E 825 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL E 825 " --> pdb=" O LEU D 816 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY E 823 " --> pdb=" O PHE D 818 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 107 through 111 removed outlier: 3.561A pdb=" N MET E 134 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL E 76 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N SER E 93 " --> pdb=" O VAL E 76 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.190A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 178 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE E 253 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR E 180 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 236 through 239 removed outlier: 3.609A pdb=" N VAL E 227 " --> pdb=" O LEU F 240 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 340 through 344 removed outlier: 3.575A pdb=" N LEU E 366 " --> pdb=" O MET E 301 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 393 through 399 removed outlier: 6.300A pdb=" N ALA E 436 " --> pdb=" O VAL E 421 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N VAL E 421 " --> pdb=" O ALA E 436 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE E 451 " --> pdb=" O TYR E 498 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 458 through 460 Processing sheet with id=AE7, first strand: chain 'E' and resid 517 through 521 removed outlier: 3.776A pdb=" N VAL E 517 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP E 554 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL E 546 " --> pdb=" O ASP E 554 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASP E 556 " --> pdb=" O ILE E 544 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL E 532 " --> pdb=" O ILE E 603 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE E 605 " --> pdb=" O VAL E 532 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU E 534 " --> pdb=" O PHE E 605 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N PHE E 573 " --> pdb=" O TYR E 624 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ARG E 621 " --> pdb=" O SER E 518 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 588 through 591 Processing sheet with id=AE9, first strand: chain 'E' and resid 695 through 698 removed outlier: 6.737A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU E 668 " --> pdb=" O GLU E 674 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU E 674 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 749 through 754 removed outlier: 6.461A pdb=" N ARG E 793 " --> pdb=" O VAL E 776 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL E 776 " --> pdb=" O ARG E 793 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE E 840 " --> pdb=" O LEU E 767 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 816 through 818 removed outlier: 3.951A pdb=" N LEU E 816 " --> pdb=" O VAL F 825 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL F 825 " --> pdb=" O LEU E 816 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY F 823 " --> pdb=" O PHE E 818 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 107 through 111 removed outlier: 3.540A pdb=" N MET F 134 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N VAL F 76 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N SER F 93 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.206A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU F 178 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE F 253 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR F 180 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA F 250 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N PHE F 268 " --> pdb=" O MET F 162 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS F 164 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LEU F 270 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN F 166 " --> pdb=" O LEU F 270 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 340 through 344 removed outlier: 3.542A pdb=" N LEU F 366 " --> pdb=" O MET F 301 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 450 through 453 removed outlier: 6.490A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL F 421 " --> pdb=" O ALA F 436 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ALA F 436 " --> pdb=" O VAL F 421 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 458 through 460 Processing sheet with id=AF8, first strand: chain 'F' and resid 517 through 521 removed outlier: 5.930A pdb=" N HIS F 558 " --> pdb=" O VAL F 543 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL F 543 " --> pdb=" O HIS F 558 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL F 532 " --> pdb=" O ILE F 603 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N PHE F 605 " --> pdb=" O VAL F 532 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU F 534 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ASN F 607 " --> pdb=" O LEU F 534 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 695 through 698 removed outlier: 6.717A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N LEU F 668 " --> pdb=" O GLU F 674 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU F 674 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 749 through 754 removed outlier: 6.457A pdb=" N ARG F 793 " --> pdb=" O VAL F 776 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL F 776 " --> pdb=" O ARG F 793 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE F 840 " --> pdb=" O LEU F 767 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 816 through 818 removed outlier: 3.998A pdb=" N LEU F 816 " --> pdb=" O VAL G 825 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL G 825 " --> pdb=" O LEU F 816 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY G 823 " --> pdb=" O PHE F 818 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 107 through 111 removed outlier: 3.564A pdb=" N MET G 134 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL G 66 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N VAL G 76 " --> pdb=" O SER G 93 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N SER G 93 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 161 through 167 removed outlier: 6.191A pdb=" N LEU G 206 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL G 189 " --> pdb=" O LEU G 206 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 179 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE G 221 " --> pdb=" O TYR G 271 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU G 270 " --> pdb=" O GLN G 166 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 340 through 344 removed outlier: 3.553A pdb=" N LEU G 366 " --> pdb=" O MET G 301 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU G 300 " --> pdb=" O VAL G 307 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU G 310 " --> pdb=" O THR G 326 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR G 326 " --> pdb=" O LEU G 310 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N PHE G 377 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS G 284 " --> pdb=" O PHE G 377 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 393 through 399 removed outlier: 6.294A pdb=" N ALA G 436 " --> pdb=" O VAL G 421 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL G 421 " --> pdb=" O ALA G 436 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU G 411 " --> pdb=" O VAL G 418 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE G 451 " --> pdb=" O TYR G 498 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 458 through 460 Processing sheet with id=AG8, first strand: chain 'G' and resid 517 through 521 removed outlier: 6.497A pdb=" N ASP G 554 " --> pdb=" O VAL G 546 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL G 546 " --> pdb=" O ASP G 554 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASP G 556 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL G 533 " --> pdb=" O VAL G 540 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N VAL G 532 " --> pdb=" O ILE G 603 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N PHE G 605 " --> pdb=" O VAL G 532 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU G 534 " --> pdb=" O PHE G 605 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE G 573 " --> pdb=" O TYR G 624 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 695 through 698 removed outlier: 6.740A pdb=" N ILE G 653 " --> pdb=" O ILE G 660 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS G 678 " --> pdb=" O GLN G 664 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU G 666 " --> pdb=" O GLN G 676 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLN G 676 " --> pdb=" O LEU G 666 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU G 668 " --> pdb=" O GLU G 674 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU G 674 " --> pdb=" O LEU G 668 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N PHE G 732 " --> pdb=" O GLN G 636 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR G 638 " --> pdb=" O PHE G 732 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 749 through 754 removed outlier: 6.463A pdb=" N ARG G 793 " --> pdb=" O VAL G 776 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL G 776 " --> pdb=" O ARG G 793 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU G 772 " --> pdb=" O PHE G 768 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE G 768 " --> pdb=" O GLU G 772 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 840 " --> pdb=" O LEU G 767 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N PHE G 808 " --> pdb=" O GLN G 861 " (cutoff:3.500A) 1517 hydrogen bonds defined for protein. 3645 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: 11.86 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 7033 1.30 - 1.43: 10185 1.43 - 1.55: 24921 1.55 - 1.68: 5 1.68 - 1.81: 193 Bond restraints: 42337 Sorted by residual: bond pdb=" C30 PEF A 503 " pdb=" O3 PEF A 503 " ideal model delta sigma weight residual 1.333 1.441 -0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C10 PEF A 503 " pdb=" O2 PEF A 503 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C2 PEF A 503 " pdb=" C3 PEF A 503 " ideal model delta sigma weight residual 1.515 1.570 -0.055 2.00e-02 2.50e+03 7.49e+00 bond pdb=" C1 PEF A 503 " pdb=" C2 PEF A 503 " ideal model delta sigma weight residual 1.517 1.571 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" CB VAL E 205 " pdb=" CG2 VAL E 205 " ideal model delta sigma weight residual 1.521 1.438 0.083 3.30e-02 9.18e+02 6.29e+00 ... (remaining 42332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 57271 3.28 - 6.56: 200 6.56 - 9.84: 4 9.84 - 13.12: 1 13.12 - 16.40: 1 Bond angle restraints: 57477 Sorted by residual: angle pdb=" O3P PEF A 503 " pdb=" P PEF A 503 " pdb=" O4P PEF A 503 " ideal model delta sigma weight residual 93.96 110.36 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C ILE G 544 " pdb=" N THR G 545 " pdb=" CA THR G 545 " ideal model delta sigma weight residual 121.80 114.63 7.17 1.71e+00 3.42e-01 1.76e+01 angle pdb=" O1P PEF A 503 " pdb=" P PEF A 503 " pdb=" O2P PEF A 503 " ideal model delta sigma weight residual 119.53 108.84 10.69 3.00e+00 1.11e-01 1.27e+01 angle pdb=" C31 PEF A 503 " pdb=" C30 PEF A 503 " pdb=" O3 PEF A 503 " ideal model delta sigma weight residual 111.02 120.71 -9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C11 PEF A 503 " pdb=" C10 PEF A 503 " pdb=" O2 PEF A 503 " ideal model delta sigma weight residual 111.28 120.67 -9.39 3.00e+00 1.11e-01 9.80e+00 ... (remaining 57472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 23943 14.25 - 28.50: 1142 28.50 - 42.74: 263 42.74 - 56.99: 57 56.99 - 71.24: 18 Dihedral angle restraints: 25423 sinusoidal: 10031 harmonic: 15392 Sorted by residual: dihedral pdb=" CA LYS C 446 " pdb=" C LYS C 446 " pdb=" N GLY C 447 " pdb=" CA GLY C 447 " ideal model delta harmonic sigma weight residual 180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LYS E 446 " pdb=" C LYS E 446 " pdb=" N GLY E 447 " pdb=" CA GLY E 447 " ideal model delta harmonic sigma weight residual -180.00 -160.75 -19.25 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LYS G 446 " pdb=" C LYS G 446 " pdb=" N GLY G 447 " pdb=" CA GLY G 447 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 25420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4268 0.051 - 0.102: 1803 0.102 - 0.154: 541 0.154 - 0.205: 33 0.205 - 0.256: 7 Chirality restraints: 6652 Sorted by residual: chirality pdb=" CB VAL D 205 " pdb=" CA VAL D 205 " pdb=" CG1 VAL D 205 " pdb=" CG2 VAL D 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2 PEF A 503 " pdb=" C1 PEF A 503 " pdb=" C3 PEF A 503 " pdb=" O2 PEF A 503 " both_signs ideal model delta sigma weight residual False -2.35 -2.60 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB VAL B 205 " pdb=" CA VAL B 205 " pdb=" CG1 VAL B 205 " pdb=" CG2 VAL B 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 6649 not shown) Planarity restraints: 7425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 603 " -0.026 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C ILE F 603 " 0.089 2.00e-02 2.50e+03 pdb=" O ILE F 603 " -0.034 2.00e-02 2.50e+03 pdb=" N SER F 604 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO G 27 " -0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C PRO G 27 " 0.079 2.00e-02 2.50e+03 pdb=" O PRO G 27 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE G 28 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 603 " -0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C ILE G 603 " 0.070 2.00e-02 2.50e+03 pdb=" O ILE G 603 " -0.027 2.00e-02 2.50e+03 pdb=" N SER G 604 " -0.024 2.00e-02 2.50e+03 ... (remaining 7422 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 19657 2.97 - 3.45: 35735 3.45 - 3.93: 62513 3.93 - 4.42: 68902 4.42 - 4.90: 121705 Nonbonded interactions: 308512 Sorted by model distance: nonbonded pdb=" O ILE C 38 " pdb=" OG SER C 41 " model vdw 2.482 3.040 nonbonded pdb=" O THR F 514 " pdb=" ND1 HIS F 558 " model vdw 2.496 3.120 nonbonded pdb=" O VAL A 317 " pdb=" OG SER A 321 " model vdw 2.496 3.040 nonbonded pdb=" O MET B 32 " pdb=" OG SER B 35 " model vdw 2.505 3.040 nonbonded pdb=" O ASN E 831 " pdb=" N ARG E 835 " model vdw 2.509 3.120 ... (remaining 308507 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 46 through 612 or resid 620 through 877)) selection = (chain 'C' and resid 46 through 877) selection = (chain 'D' and (resid 46 through 612 or resid 620 through 877)) selection = (chain 'E' and (resid 46 through 612 or resid 620 through 877)) selection = (chain 'F' and (resid 46 through 612 or resid 620 through 877)) selection = (chain 'G' and (resid 46 through 612 or resid 620 through 877)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.59 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 45.360 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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 : 0.012 0.108 42345 Z= 0.456 Angle : 0.665 16.396 57489 Z= 0.357 Chirality : 0.058 0.256 6652 Planarity : 0.005 0.052 7425 Dihedral : 9.220 71.239 15597 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.18 % Allowed : 4.94 % Favored : 93.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.11), residues: 5415 helix: -1.05 (0.17), residues: 843 sheet: 0.22 (0.13), residues: 1683 loop : -1.04 (0.11), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 344 TYR 0.027 0.003 TYR G 302 PHE 0.024 0.003 PHE G 221 TRP 0.025 0.002 TRP B 574 HIS 0.014 0.002 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.01160 (42337) covalent geometry : angle 0.66407 (57477) hydrogen bonds : bond 0.15647 ( 1517) hydrogen bonds : angle 6.49544 ( 3645) metal coordination : bond 0.01688 ( 8) metal coordination : angle 2.22977 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 456 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8759 (mtm) cc_final: 0.8157 (mtt) REVERT: A 260 ARG cc_start: 0.7034 (ttt180) cc_final: 0.6576 (mtp180) REVERT: A 388 MET cc_start: 0.8669 (ttp) cc_final: 0.7896 (ttp) REVERT: B 49 VAL cc_start: 0.9356 (t) cc_final: 0.9084 (m) REVERT: B 68 TYR cc_start: 0.8914 (t80) cc_final: 0.8687 (t80) REVERT: B 509 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8575 (pp) REVERT: C 154 TYR cc_start: 0.7007 (p90) cc_final: 0.6792 (p90) REVERT: C 742 SER cc_start: 0.9000 (m) cc_final: 0.8734 (t) REVERT: D 54 MET cc_start: 0.8068 (mmm) cc_final: 0.7723 (mmp) REVERT: D 143 ASP cc_start: 0.8308 (t0) cc_final: 0.8030 (t0) REVERT: E 87 LYS cc_start: 0.8435 (mttm) cc_final: 0.8215 (mmtt) REVERT: F 87 LYS cc_start: 0.8382 (mttm) cc_final: 0.8135 (mmmt) REVERT: F 142 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7924 (tp-100) REVERT: F 509 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9035 (pp) REVERT: F 779 MET cc_start: 0.8714 (mtp) cc_final: 0.8476 (mtm) REVERT: G 89 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7865 (mm-30) REVERT: G 104 GLU cc_start: 0.8971 (tt0) cc_final: 0.8687 (mt-10) REVERT: G 143 ASP cc_start: 0.8769 (t0) cc_final: 0.8490 (t0) REVERT: G 397 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.8851 (pp) outliers start: 53 outliers final: 12 residues processed: 507 average time/residue: 0.2319 time to fit residues: 195.3455 Evaluate side-chains 288 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain G residue 397 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 9.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 0.7980 chunk 414 optimal weight: 0.9980 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN B 388 HIS B 607 ASN C 144 HIS C 454 ASN D 388 HIS D 454 ASN E 454 ASN G 454 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116116 restraints weight = 163672.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.117552 restraints weight = 94080.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.117596 restraints weight = 65584.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.117782 restraints weight = 65963.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.117844 restraints weight = 59708.324| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 42345 Z= 0.106 Angle : 0.511 8.073 57489 Z= 0.267 Chirality : 0.044 0.153 6652 Planarity : 0.004 0.053 7425 Dihedral : 4.814 56.891 5899 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.16 % Allowed : 7.69 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.11), residues: 5415 helix: -0.49 (0.18), residues: 840 sheet: 0.15 (0.13), residues: 1554 loop : -0.81 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 549 TYR 0.014 0.001 TYR E 68 PHE 0.014 0.001 PHE G 145 TRP 0.008 0.001 TRP A 140 HIS 0.003 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00230 (42337) covalent geometry : angle 0.51043 (57477) hydrogen bonds : bond 0.03976 ( 1517) hydrogen bonds : angle 5.58524 ( 3645) metal coordination : bond 0.00449 ( 8) metal coordination : angle 1.11516 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7313 (mtt) cc_final: 0.6944 (mtp) REVERT: A 80 MET cc_start: 0.8867 (mtm) cc_final: 0.8593 (mtt) REVERT: A 260 ARG cc_start: 0.6998 (ttt180) cc_final: 0.6482 (mtp180) REVERT: A 388 MET cc_start: 0.8468 (ttp) cc_final: 0.8038 (ttp) REVERT: B 104 GLU cc_start: 0.8966 (tt0) cc_final: 0.8385 (mt-10) REVERT: B 509 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8568 (pp) REVERT: B 820 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6884 (mm) REVERT: C 87 LYS cc_start: 0.8616 (mmmt) cc_final: 0.8095 (mmmm) REVERT: C 142 GLN cc_start: 0.9102 (tp-100) cc_final: 0.8870 (tp-100) REVERT: C 154 TYR cc_start: 0.7293 (p90) cc_final: 0.7033 (p90) REVERT: C 742 SER cc_start: 0.8905 (m) cc_final: 0.8667 (t) REVERT: D 142 GLN cc_start: 0.8304 (tp-100) cc_final: 0.7995 (tp-100) REVERT: D 143 ASP cc_start: 0.8272 (t0) cc_final: 0.7926 (p0) REVERT: D 145 PHE cc_start: 0.8987 (m-80) cc_final: 0.8772 (m-10) REVERT: E 89 GLU cc_start: 0.7496 (mp0) cc_final: 0.7263 (mp0) REVERT: E 135 MET cc_start: 0.7426 (tpp) cc_final: 0.6770 (tpp) REVERT: F 87 LYS cc_start: 0.8342 (mttm) cc_final: 0.8081 (mmmt) REVERT: F 142 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7867 (tp-100) REVERT: F 143 ASP cc_start: 0.8446 (t0) cc_final: 0.8201 (t0) REVERT: G 87 LYS cc_start: 0.8584 (mttp) cc_final: 0.7991 (mtpp) REVERT: G 89 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7641 (mm-30) REVERT: G 91 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8452 (ttmm) REVERT: G 104 GLU cc_start: 0.9009 (tt0) cc_final: 0.8663 (mt-10) REVERT: G 143 ASP cc_start: 0.8864 (t0) cc_final: 0.8584 (t0) REVERT: G 162 MET cc_start: 0.8522 (tpp) cc_final: 0.8270 (tpp) outliers start: 52 outliers final: 22 residues processed: 334 average time/residue: 0.2142 time to fit residues: 123.2740 Evaluate side-chains 288 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 264 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 607 ASN Chi-restraints excluded: chain B residue 820 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain F residue 532 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 295 optimal weight: 1.9990 chunk 476 optimal weight: 0.9980 chunk 133 optimal weight: 10.0000 chunk 512 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 488 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 221 optimal weight: 10.0000 chunk 391 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 HIS F 309 GLN F 640 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.133932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.114357 restraints weight = 159895.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.116178 restraints weight = 106095.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.116498 restraints weight = 66832.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.116654 restraints weight = 66957.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.116853 restraints weight = 59112.025| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42345 Z= 0.151 Angle : 0.527 9.174 57489 Z= 0.275 Chirality : 0.045 0.266 6652 Planarity : 0.004 0.043 7425 Dihedral : 4.790 54.655 5888 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.68 % Allowed : 8.07 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.11), residues: 5415 helix: -0.08 (0.19), residues: 807 sheet: 0.09 (0.13), residues: 1509 loop : -0.72 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 549 TYR 0.012 0.001 TYR C 302 PHE 0.020 0.002 PHE B 605 TRP 0.008 0.001 TRP D 809 HIS 0.005 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00349 (42337) covalent geometry : angle 0.52622 (57477) hydrogen bonds : bond 0.03591 ( 1517) hydrogen bonds : angle 5.39678 ( 3645) metal coordination : bond 0.00676 ( 8) metal coordination : angle 1.88858 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 283 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7484 (mtt) cc_final: 0.7224 (mtp) REVERT: A 80 MET cc_start: 0.8900 (mtm) cc_final: 0.8295 (mtt) REVERT: A 260 ARG cc_start: 0.7078 (ttt180) cc_final: 0.6577 (mtp180) REVERT: A 401 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 509 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8612 (pp) REVERT: C 87 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8159 (mmmm) REVERT: C 142 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8845 (tp-100) REVERT: C 154 TYR cc_start: 0.7493 (p90) cc_final: 0.7258 (p90) REVERT: C 742 SER cc_start: 0.8914 (m) cc_final: 0.8652 (t) REVERT: E 87 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7789 (mmmt) REVERT: E 89 GLU cc_start: 0.7752 (mp0) cc_final: 0.7463 (mp0) REVERT: E 764 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.9001 (m) REVERT: F 87 LYS cc_start: 0.8331 (mttm) cc_final: 0.8093 (mmmt) REVERT: F 135 MET cc_start: 0.7942 (tpp) cc_final: 0.7587 (tpp) REVERT: F 142 GLN cc_start: 0.8329 (tp-100) cc_final: 0.7962 (tp-100) REVERT: F 143 ASP cc_start: 0.8600 (t0) cc_final: 0.8278 (t0) REVERT: G 51 ILE cc_start: 0.8900 (mt) cc_final: 0.8599 (pt) REVERT: G 87 LYS cc_start: 0.8568 (mttp) cc_final: 0.7959 (mtpp) REVERT: G 89 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7449 (mm-30) REVERT: G 91 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8440 (ttmm) REVERT: G 143 ASP cc_start: 0.8975 (t0) cc_final: 0.8647 (t0) REVERT: G 557 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9060 (pp) outliers start: 75 outliers final: 37 residues processed: 344 average time/residue: 0.2323 time to fit residues: 136.7945 Evaluate side-chains 292 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 764 THR Chi-restraints excluded: chain D residue 224 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 517 VAL Chi-restraints excluded: chain D residue 821 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 764 THR Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 821 THR Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 807 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 15 optimal weight: 0.3980 chunk 311 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 394 optimal weight: 0.8980 chunk 499 optimal weight: 5.9990 chunk 440 optimal weight: 5.9990 chunk 263 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 359 optimal weight: 0.0370 chunk 416 optimal weight: 0.0370 chunk 213 optimal weight: 8.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 HIS C 640 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.116858 restraints weight = 159673.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.117381 restraints weight = 103215.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.117379 restraints weight = 81236.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.117579 restraints weight = 80950.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118093 restraints weight = 68976.459| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 42345 Z= 0.081 Angle : 0.480 8.691 57489 Z= 0.247 Chirality : 0.044 0.149 6652 Planarity : 0.003 0.044 7425 Dihedral : 4.409 53.842 5884 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.56 % Allowed : 8.52 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.11), residues: 5415 helix: 0.03 (0.19), residues: 800 sheet: 0.21 (0.14), residues: 1479 loop : -0.69 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 549 TYR 0.011 0.001 TYR B 68 PHE 0.011 0.001 PHE G 145 TRP 0.007 0.001 TRP D 809 HIS 0.002 0.000 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00167 (42337) covalent geometry : angle 0.47973 (57477) hydrogen bonds : bond 0.02884 ( 1517) hydrogen bonds : angle 5.16216 ( 3645) metal coordination : bond 0.00317 ( 8) metal coordination : angle 1.85319 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 273 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8841 (mtm) cc_final: 0.8232 (mtt) REVERT: A 109 MET cc_start: 0.8594 (mmm) cc_final: 0.8327 (mmm) REVERT: A 200 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6915 (tp) REVERT: A 260 ARG cc_start: 0.7038 (ttt180) cc_final: 0.6477 (mtp180) REVERT: B 509 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8652 (pp) REVERT: B 821 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6767 (m) REVERT: C 87 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8128 (mmmm) REVERT: C 142 GLN cc_start: 0.9029 (tp-100) cc_final: 0.8749 (tp-100) REVERT: C 742 SER cc_start: 0.8890 (m) cc_final: 0.8626 (t) REVERT: D 87 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7729 (mmmt) REVERT: E 87 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7798 (mmmt) REVERT: E 89 GLU cc_start: 0.7714 (mp0) cc_final: 0.7379 (mp0) REVERT: E 91 LYS cc_start: 0.9367 (ttmm) cc_final: 0.9140 (ttmm) REVERT: F 87 LYS cc_start: 0.8366 (mttm) cc_final: 0.8108 (mmmt) REVERT: F 131 TYR cc_start: 0.8827 (p90) cc_final: 0.8548 (p90) REVERT: F 135 MET cc_start: 0.7878 (tpp) cc_final: 0.7551 (tpp) REVERT: F 142 GLN cc_start: 0.8370 (tp-100) cc_final: 0.7860 (tp-100) REVERT: F 143 ASP cc_start: 0.8587 (t0) cc_final: 0.8249 (t0) REVERT: G 87 LYS cc_start: 0.8532 (mttp) cc_final: 0.7915 (mtpp) REVERT: G 89 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7468 (mm-30) REVERT: G 91 LYS cc_start: 0.8692 (mtpp) cc_final: 0.8436 (ttmm) REVERT: G 557 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8974 (pp) outliers start: 70 outliers final: 28 residues processed: 331 average time/residue: 0.2301 time to fit residues: 131.1127 Evaluate side-chains 286 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 254 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 517 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 557 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 209 optimal weight: 40.0000 chunk 506 optimal weight: 20.0000 chunk 303 optimal weight: 0.8980 chunk 437 optimal weight: 10.0000 chunk 363 optimal weight: 0.7980 chunk 484 optimal weight: 0.8980 chunk 388 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 389 optimal weight: 0.8980 chunk 378 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 582 GLN E 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.134214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.115630 restraints weight = 158169.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.116125 restraints weight = 105566.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.116404 restraints weight = 80294.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.116552 restraints weight = 79678.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.116883 restraints weight = 67083.358| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 42345 Z= 0.095 Angle : 0.484 9.566 57489 Z= 0.248 Chirality : 0.044 0.246 6652 Planarity : 0.003 0.043 7425 Dihedral : 4.303 54.507 5881 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.36 % Allowed : 8.90 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.11), residues: 5415 helix: 0.11 (0.19), residues: 812 sheet: 0.24 (0.14), residues: 1506 loop : -0.67 (0.11), residues: 3097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 53 TYR 0.007 0.001 TYR D 131 PHE 0.018 0.001 PHE G 53 TRP 0.007 0.001 TRP D 809 HIS 0.003 0.000 HIS G 164 Details of bonding type rmsd covalent geometry : bond 0.00213 (42337) covalent geometry : angle 0.48332 (57477) hydrogen bonds : bond 0.02943 ( 1517) hydrogen bonds : angle 5.10542 ( 3645) metal coordination : bond 0.00523 ( 8) metal coordination : angle 1.92551 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 269 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8813 (mtm) cc_final: 0.8186 (mtt) REVERT: A 109 MET cc_start: 0.8657 (mmm) cc_final: 0.8370 (mmm) REVERT: A 120 MET cc_start: 0.7843 (ptt) cc_final: 0.7533 (ptp) REVERT: A 200 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6821 (tp) REVERT: A 260 ARG cc_start: 0.6991 (ttt180) cc_final: 0.6490 (mtp180) REVERT: B 509 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8652 (pp) REVERT: C 87 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8148 (mmmm) REVERT: C 142 GLN cc_start: 0.9026 (tp-100) cc_final: 0.8782 (tp-100) REVERT: C 742 SER cc_start: 0.8930 (m) cc_final: 0.8659 (t) REVERT: C 816 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5772 (pp) REVERT: E 87 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7853 (mmmt) REVERT: E 89 GLU cc_start: 0.7798 (mp0) cc_final: 0.7387 (mp0) REVERT: F 63 ARG cc_start: 0.6552 (ppt170) cc_final: 0.6328 (ppt170) REVERT: F 87 LYS cc_start: 0.8368 (mttm) cc_final: 0.8105 (mmmt) REVERT: F 135 MET cc_start: 0.7863 (tpp) cc_final: 0.7577 (tpp) REVERT: F 142 GLN cc_start: 0.8334 (tp-100) cc_final: 0.7871 (tp-100) REVERT: F 143 ASP cc_start: 0.8621 (t0) cc_final: 0.8275 (t0) REVERT: G 89 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7487 (mm-30) REVERT: G 551 ASN cc_start: 0.8907 (p0) cc_final: 0.8642 (p0) REVERT: G 557 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8993 (pp) outliers start: 61 outliers final: 43 residues processed: 314 average time/residue: 0.2173 time to fit residues: 117.2177 Evaluate side-chains 302 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 532 VAL Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 807 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 0 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 537 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 533 optimal weight: 0.9990 chunk 525 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 191 optimal weight: 0.0670 chunk 430 optimal weight: 9.9990 chunk 435 optimal weight: 2.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 HIS E 77 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.113924 restraints weight = 160459.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.115326 restraints weight = 94810.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.116205 restraints weight = 68769.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.116895 restraints weight = 56961.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.117117 restraints weight = 49445.694| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42345 Z= 0.112 Angle : 0.494 8.506 57489 Z= 0.255 Chirality : 0.045 0.215 6652 Planarity : 0.003 0.045 7425 Dihedral : 4.381 55.059 5881 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.45 % Allowed : 9.19 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.11), residues: 5415 helix: 0.17 (0.19), residues: 816 sheet: 0.30 (0.14), residues: 1512 loop : -0.69 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 729 TYR 0.008 0.001 TYR C 302 PHE 0.016 0.001 PHE G 145 TRP 0.007 0.001 TRP A 415 HIS 0.003 0.000 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00258 (42337) covalent geometry : angle 0.49303 (57477) hydrogen bonds : bond 0.03062 ( 1517) hydrogen bonds : angle 5.11020 ( 3645) metal coordination : bond 0.00557 ( 8) metal coordination : angle 1.94933 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 262 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8922 (mtm) cc_final: 0.8299 (mtt) REVERT: A 120 MET cc_start: 0.7890 (ptt) cc_final: 0.7639 (ptp) REVERT: A 260 ARG cc_start: 0.7015 (ttt180) cc_final: 0.6496 (mtp180) REVERT: B 509 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8564 (pp) REVERT: B 821 THR cc_start: 0.6965 (OUTLIER) cc_final: 0.6683 (m) REVERT: C 87 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8217 (mmmm) REVERT: C 105 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7356 (tm-30) REVERT: C 742 SER cc_start: 0.8885 (m) cc_final: 0.8622 (t) REVERT: D 75 THR cc_start: 0.9157 (m) cc_final: 0.8939 (p) REVERT: D 87 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7836 (mmmt) REVERT: E 49 VAL cc_start: 0.9332 (OUTLIER) cc_final: 0.9093 (p) REVERT: E 87 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7857 (mmmt) REVERT: E 89 GLU cc_start: 0.7994 (mp0) cc_final: 0.7593 (mp0) REVERT: F 63 ARG cc_start: 0.6729 (ppt170) cc_final: 0.6478 (ppt170) REVERT: F 135 MET cc_start: 0.7984 (tpp) cc_final: 0.7657 (tpp) REVERT: F 142 GLN cc_start: 0.8293 (tp-100) cc_final: 0.7897 (tp-100) REVERT: F 143 ASP cc_start: 0.8556 (t0) cc_final: 0.8248 (t0) REVERT: F 816 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7039 (pp) REVERT: G 87 LYS cc_start: 0.8490 (mttp) cc_final: 0.7927 (mtpp) REVERT: G 89 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7475 (mm-30) REVERT: G 143 ASP cc_start: 0.8601 (t0) cc_final: 0.8351 (t0) REVERT: G 549 ARG cc_start: 0.7780 (ttp-110) cc_final: 0.7566 (ttp-110) REVERT: G 551 ASN cc_start: 0.8784 (p0) cc_final: 0.8529 (p0) REVERT: G 557 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9086 (pp) outliers start: 65 outliers final: 42 residues processed: 316 average time/residue: 0.2209 time to fit residues: 118.7890 Evaluate side-chains 298 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 251 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 767 LEU Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 807 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 313 optimal weight: 6.9990 chunk 327 optimal weight: 7.9990 chunk 403 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 187 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 364 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 519 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.112538 restraints weight = 160743.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.113976 restraints weight = 94022.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.114856 restraints weight = 67883.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.115528 restraints weight = 56119.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.115853 restraints weight = 48837.662| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 42345 Z= 0.105 Angle : 0.496 10.852 57489 Z= 0.255 Chirality : 0.044 0.178 6652 Planarity : 0.003 0.045 7425 Dihedral : 4.351 54.667 5880 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.48 % Allowed : 9.26 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.11), residues: 5415 helix: 0.27 (0.19), residues: 803 sheet: 0.31 (0.14), residues: 1530 loop : -0.66 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 729 TYR 0.013 0.001 TYR B 68 PHE 0.012 0.001 PHE E 253 TRP 0.007 0.001 TRP D 809 HIS 0.002 0.000 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00239 (42337) covalent geometry : angle 0.49550 (57477) hydrogen bonds : bond 0.02981 ( 1517) hydrogen bonds : angle 5.08071 ( 3645) metal coordination : bond 0.00504 ( 8) metal coordination : angle 1.98718 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 249 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8905 (mtm) cc_final: 0.8271 (mtt) REVERT: A 260 ARG cc_start: 0.6993 (ttt180) cc_final: 0.6455 (mtp180) REVERT: B 342 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: B 509 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8546 (pp) REVERT: B 821 THR cc_start: 0.7050 (OUTLIER) cc_final: 0.6769 (m) REVERT: C 87 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8156 (mmmm) REVERT: C 105 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 651 MET cc_start: 0.9349 (ttm) cc_final: 0.9141 (ttm) REVERT: C 742 SER cc_start: 0.8880 (m) cc_final: 0.8622 (t) REVERT: D 87 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7779 (mmmt) REVERT: E 49 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9092 (p) REVERT: E 87 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7876 (mmmt) REVERT: F 63 ARG cc_start: 0.6542 (ppt170) cc_final: 0.6303 (ppt170) REVERT: F 87 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7614 (mmmt) REVERT: F 135 MET cc_start: 0.8013 (tpp) cc_final: 0.7644 (tpp) REVERT: F 142 GLN cc_start: 0.8305 (tp-100) cc_final: 0.7906 (tp-100) REVERT: F 143 ASP cc_start: 0.8581 (t0) cc_final: 0.8302 (t0) REVERT: F 816 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6882 (pp) REVERT: G 87 LYS cc_start: 0.8486 (mttp) cc_final: 0.7926 (mtpp) REVERT: G 89 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7408 (mm-30) REVERT: G 143 ASP cc_start: 0.8623 (t0) cc_final: 0.8342 (t0) REVERT: G 551 ASN cc_start: 0.8802 (p0) cc_final: 0.8573 (p0) REVERT: G 557 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9015 (pp) outliers start: 66 outliers final: 47 residues processed: 300 average time/residue: 0.2209 time to fit residues: 112.6855 Evaluate side-chains 294 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 241 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 557 LEU Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 488 LYS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 342 GLU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain E residue 567 LEU Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 807 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 47 optimal weight: 10.0000 chunk 234 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 523 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 516 optimal weight: 0.4980 chunk 178 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 513 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 GLN E 454 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.130955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.111005 restraints weight = 160766.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.112432 restraints weight = 95021.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.113366 restraints weight = 68906.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.113878 restraints weight = 56435.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.114462 restraints weight = 49729.491| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 42345 Z= 0.160 Angle : 0.536 10.113 57489 Z= 0.277 Chirality : 0.046 0.215 6652 Planarity : 0.004 0.046 7425 Dihedral : 4.631 55.832 5880 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.94 % Rotamer: Outliers : 1.41 % Allowed : 9.46 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.11), residues: 5415 helix: 0.22 (0.19), residues: 806 sheet: 0.29 (0.13), residues: 1559 loop : -0.72 (0.11), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 729 TYR 0.011 0.001 TYR F 302 PHE 0.015 0.001 PHE C 253 TRP 0.012 0.001 TRP A 415 HIS 0.004 0.001 HIS B 164 Details of bonding type rmsd covalent geometry : bond 0.00375 (42337) covalent geometry : angle 0.53500 (57477) hydrogen bonds : bond 0.03459 ( 1517) hydrogen bonds : angle 5.25345 ( 3645) metal coordination : bond 0.00908 ( 8) metal coordination : angle 2.60976 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.7127 (mtt) cc_final: 0.6889 (mtt) REVERT: A 80 MET cc_start: 0.8967 (mtm) cc_final: 0.8358 (mtt) REVERT: A 230 LEU cc_start: 0.8921 (mp) cc_final: 0.8712 (mt) REVERT: A 260 ARG cc_start: 0.7059 (ttt180) cc_final: 0.6442 (mtp180) REVERT: B 342 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8536 (pm20) REVERT: B 509 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8554 (pp) REVERT: B 821 THR cc_start: 0.6968 (OUTLIER) cc_final: 0.6684 (m) REVERT: C 87 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8340 (mmmm) REVERT: C 105 GLU cc_start: 0.7790 (tm-30) cc_final: 0.7572 (tm-30) REVERT: C 517 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8829 (p) REVERT: C 651 MET cc_start: 0.9348 (ttm) cc_final: 0.9139 (ttm) REVERT: C 742 SER cc_start: 0.8942 (m) cc_final: 0.8673 (t) REVERT: E 87 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7552 (mmmt) REVERT: E 372 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: F 63 ARG cc_start: 0.6726 (ppt170) cc_final: 0.6472 (ppt170) REVERT: F 87 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7640 (mmmt) REVERT: F 135 MET cc_start: 0.8147 (tpp) cc_final: 0.7743 (tpp) REVERT: F 142 GLN cc_start: 0.8385 (tp-100) cc_final: 0.7977 (tp-100) REVERT: F 816 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6930 (pp) REVERT: G 87 LYS cc_start: 0.8500 (mttp) cc_final: 0.7950 (mtpp) REVERT: G 89 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7424 (mm-30) REVERT: G 105 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7885 (pt0) REVERT: G 143 ASP cc_start: 0.8676 (t0) cc_final: 0.8389 (t0) REVERT: G 549 ARG cc_start: 0.7882 (ttp-110) cc_final: 0.7680 (ttp-110) REVERT: G 557 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9034 (pp) outliers start: 63 outliers final: 39 residues processed: 293 average time/residue: 0.2134 time to fit residues: 107.0101 Evaluate side-chains 280 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 104 GLU Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 807 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 184 optimal weight: 9.9990 chunk 479 optimal weight: 1.9990 chunk 469 optimal weight: 9.9990 chunk 504 optimal weight: 5.9990 chunk 289 optimal weight: 9.9990 chunk 145 optimal weight: 0.0970 chunk 47 optimal weight: 9.9990 chunk 417 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 281 optimal weight: 0.0070 chunk 391 optimal weight: 3.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 GLN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 591 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.111738 restraints weight = 162880.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.113226 restraints weight = 95169.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.114250 restraints weight = 68699.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.114960 restraints weight = 55519.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115294 restraints weight = 48402.460| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 42345 Z= 0.108 Angle : 0.509 7.746 57489 Z= 0.261 Chirality : 0.045 0.186 6652 Planarity : 0.003 0.046 7425 Dihedral : 4.483 54.678 5880 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.27 % Allowed : 9.84 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.11), residues: 5415 helix: 0.36 (0.20), residues: 788 sheet: 0.30 (0.14), residues: 1517 loop : -0.67 (0.11), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.008 0.001 TYR B 68 PHE 0.013 0.001 PHE G 53 TRP 0.012 0.001 TRP A 415 HIS 0.006 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00247 (42337) covalent geometry : angle 0.50737 (57477) hydrogen bonds : bond 0.03090 ( 1517) hydrogen bonds : angle 5.15319 ( 3645) metal coordination : bond 0.00673 ( 8) metal coordination : angle 2.99134 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 247 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 ARG cc_start: 0.7043 (ttt180) cc_final: 0.6410 (mtp180) REVERT: B 342 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: B 509 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8406 (pp) REVERT: B 821 THR cc_start: 0.6921 (OUTLIER) cc_final: 0.6635 (m) REVERT: C 87 LYS cc_start: 0.8688 (mmmt) cc_final: 0.8182 (mmmm) REVERT: C 517 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8889 (p) REVERT: C 742 SER cc_start: 0.8916 (m) cc_final: 0.8662 (t) REVERT: D 87 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7525 (mmmt) REVERT: D 397 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9028 (pp) REVERT: E 87 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7950 (mmmt) REVERT: E 372 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: F 63 ARG cc_start: 0.6739 (ppt170) cc_final: 0.6512 (ppt170) REVERT: F 87 LYS cc_start: 0.7961 (mmmt) cc_final: 0.7707 (mmmt) REVERT: F 135 MET cc_start: 0.8176 (tpp) cc_final: 0.7770 (tpp) REVERT: F 142 GLN cc_start: 0.8362 (tp-100) cc_final: 0.7965 (tp-100) REVERT: F 816 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.7001 (pp) REVERT: G 87 LYS cc_start: 0.8475 (mttp) cc_final: 0.7925 (mtpp) REVERT: G 89 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7371 (mm-30) REVERT: G 143 ASP cc_start: 0.8631 (t0) cc_final: 0.8334 (t0) REVERT: G 557 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9043 (pp) outliers start: 57 outliers final: 42 residues processed: 293 average time/residue: 0.2294 time to fit residues: 114.4847 Evaluate side-chains 291 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 241 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 488 LYS Chi-restraints excluded: chain C residue 491 MET Chi-restraints excluded: chain C residue 517 VAL Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 488 LYS Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 435 optimal weight: 1.9990 chunk 370 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 218 optimal weight: 30.0000 chunk 349 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 chunk 433 optimal weight: 7.9990 chunk 487 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 326 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 857 HIS F 857 HIS G 454 ASN G 591 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.129712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.109399 restraints weight = 164022.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.110810 restraints weight = 98659.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.111756 restraints weight = 71818.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.112298 restraints weight = 58648.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.112780 restraints weight = 51891.802| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 42345 Z= 0.307 Angle : 0.650 8.812 57489 Z= 0.337 Chirality : 0.050 0.183 6652 Planarity : 0.004 0.044 7425 Dihedral : 5.182 65.864 5880 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.58 % Favored : 95.31 % Rotamer: Outliers : 1.30 % Allowed : 9.77 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.11), residues: 5415 helix: 0.14 (0.20), residues: 793 sheet: 0.19 (0.13), residues: 1562 loop : -0.82 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 220 TYR 0.020 0.002 TYR F 302 PHE 0.018 0.002 PHE D 253 TRP 0.015 0.001 TRP A 84 HIS 0.006 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00738 (42337) covalent geometry : angle 0.64733 (57477) hydrogen bonds : bond 0.04270 ( 1517) hydrogen bonds : angle 5.57409 ( 3645) metal coordination : bond 0.01312 ( 8) metal coordination : angle 3.88797 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10830 Ramachandran restraints generated. 5415 Oldfield, 0 Emsley, 5415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 247 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8894 (mtm) cc_final: 0.8691 (mtt) REVERT: A 245 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7395 (tpm170) REVERT: A 260 ARG cc_start: 0.7008 (ttt180) cc_final: 0.6377 (mtp180) REVERT: A 326 PHE cc_start: 0.7263 (m-80) cc_final: 0.6569 (m-80) REVERT: B 135 MET cc_start: 0.6254 (ttp) cc_final: 0.5986 (ttp) REVERT: B 342 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: B 821 THR cc_start: 0.6930 (OUTLIER) cc_final: 0.6659 (m) REVERT: C 87 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8312 (mmmm) REVERT: C 142 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8151 (tp40) REVERT: C 742 SER cc_start: 0.9006 (m) cc_final: 0.8749 (t) REVERT: D 87 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7827 (mmmt) REVERT: E 87 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7787 (mmmt) REVERT: F 87 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7778 (mmmt) REVERT: F 135 MET cc_start: 0.8274 (tpp) cc_final: 0.7795 (tpp) REVERT: F 142 GLN cc_start: 0.8508 (tp-100) cc_final: 0.8106 (tp-100) REVERT: F 816 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6971 (pp) REVERT: G 63 ARG cc_start: 0.8184 (ptt90) cc_final: 0.7021 (ppt170) REVERT: G 87 LYS cc_start: 0.8474 (mttp) cc_final: 0.7909 (mtpp) REVERT: G 89 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7382 (mm-30) REVERT: G 105 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7775 (pt0) REVERT: G 143 ASP cc_start: 0.8634 (t0) cc_final: 0.8395 (t0) REVERT: G 557 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9128 (pp) outliers start: 58 outliers final: 38 residues processed: 292 average time/residue: 0.2301 time to fit residues: 113.7829 Evaluate side-chains 283 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 266 CYS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 408 TRP Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 567 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain B residue 821 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 745 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 517 VAL Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain F residue 342 GLU Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 816 LEU Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 557 LEU Chi-restraints excluded: chain G residue 807 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 541 random chunks: chunk 410 optimal weight: 0.0970 chunk 530 optimal weight: 3.9990 chunk 407 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 340 optimal weight: 0.8980 chunk 539 optimal weight: 9.9990 chunk 235 optimal weight: 0.8980 chunk 419 optimal weight: 2.9990 chunk 444 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.130792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.110787 restraints weight = 162951.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.112202 restraints weight = 95249.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.113195 restraints weight = 68537.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.113852 restraints weight = 55274.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.114166 restraints weight = 48150.441| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42345 Z= 0.133 Angle : 0.546 10.655 57489 Z= 0.281 Chirality : 0.045 0.178 6652 Planarity : 0.003 0.046 7425 Dihedral : 4.833 64.024 5880 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.03 % Allowed : 10.11 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.11), residues: 5415 helix: 0.38 (0.20), residues: 778 sheet: 0.22 (0.14), residues: 1490 loop : -0.78 (0.11), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 67 TYR 0.009 0.001 TYR F 302 PHE 0.013 0.001 PHE E 253 TRP 0.013 0.001 TRP A 415 HIS 0.003 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00307 (42337) covalent geometry : angle 0.54359 (57477) hydrogen bonds : bond 0.03424 ( 1517) hydrogen bonds : angle 5.36390 ( 3645) metal coordination : bond 0.00805 ( 8) metal coordination : angle 3.39728 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6426.04 seconds wall clock time: 111 minutes 47.18 seconds (6707.18 seconds total)