Starting phenix.real_space_refine on Sun Jun 7 04:12:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9r8w_53844/06_2026/9r8w_53844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9r8w_53844/06_2026/9r8w_53844.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 { model { file = "/net/cci-nas-00/data/ceres_data/9r8w_53844/06_2026/9r8w_53844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9r8w_53844/06_2026/9r8w_53844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9r8w_53844/06_2026/9r8w_53844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9r8w_53844/06_2026/9r8w_53844.map" } 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 204 5.16 5 C 21199 2.51 5 N 5713 2.21 5 O 6258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33382 Number of models: 1 Model: "" Number of chains: 12 Chain: "Q" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 587 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "R" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 587 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "S" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 587 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "A" Number of atoms: 7722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7722 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 34, 'TRANS': 936} Chain breaks: 1 Chain: "B" Number of atoms: 7737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7737 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 34, 'TRANS': 939} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 7722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7722 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 34, 'TRANS': 936} Chain breaks: 1 Chain: "D" Number of atoms: 7745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 974, 7745 Classifications: {'peptide': 974} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 34, 'TRANS': 939} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 587 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.17, per 1000 atoms: 0.27 Number of scatterers: 33382 At special positions: 0 Unit cell: (194.58, 197.892, 139.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 8 15.00 O 6258 8.00 N 5713 7.00 C 21199 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS Q 47 " - pdb=" SG CYS Q 99 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 50 " - pdb=" SG CYS Q 93 " distance=2.03 Simple disulfide: pdb=" SG CYS R 47 " - pdb=" SG CYS R 99 " distance=2.03 Simple disulfide: pdb=" SG CYS R 50 " - pdb=" SG CYS R 93 " distance=2.03 Simple disulfide: pdb=" SG CYS S 47 " - pdb=" SG CYS S 99 " distance=2.03 Simple disulfide: pdb=" SG CYS S 50 " - pdb=" SG CYS S 93 " distance=2.03 Simple disulfide: pdb=" SG CYS A 794 " - pdb=" SG CYS A 815 " distance=2.03 Simple disulfide: pdb=" SG CYS B 794 " - pdb=" SG CYS B 815 " distance=2.03 Simple disulfide: pdb=" SG CYS P 47 " - pdb=" SG CYS P 99 " distance=2.03 Simple disulfide: pdb=" SG CYS P 50 " - pdb=" SG CYS P 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.3 seconds 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7980 Finding SS restraints... Secondary structure from input PDB file: 137 helices and 37 sheets defined 35.7% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'Q' and resid 44 through 56 removed outlier: 3.548A pdb=" N CYS Q 50 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE Q 54 " --> pdb=" O CYS Q 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA Q 55 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 93 removed outlier: 3.508A pdb=" N LEU Q 91 " --> pdb=" O ILE Q 87 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS Q 93 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 100 Processing helix chain 'R' and resid 43 through 54 removed outlier: 4.360A pdb=" N CYS R 47 " --> pdb=" O ASP R 43 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS R 50 " --> pdb=" O ARG R 46 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE R 54 " --> pdb=" O CYS R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 removed outlier: 3.785A pdb=" N CYS R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 54 removed outlier: 3.523A pdb=" N CYS S 50 " --> pdb=" O ARG S 46 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU S 51 " --> pdb=" O CYS S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 93 removed outlier: 4.115A pdb=" N PHE S 86 " --> pdb=" O GLN S 82 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU S 91 " --> pdb=" O ILE S 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.663A pdb=" N HIS A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 64 removed outlier: 4.399A pdb=" N ALA A 58 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY A 64 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.617A pdb=" N LEU A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 149 Processing helix chain 'A' and resid 159 through 177 removed outlier: 3.727A pdb=" N VAL A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 185 removed outlier: 3.796A pdb=" N ASP A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP A 185 " --> pdb=" O ASP A 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 181 through 185' Processing helix chain 'A' and resid 188 through 201 removed outlier: 4.009A pdb=" N HIS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 232 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.595A pdb=" N ILE A 250 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 271 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.634A pdb=" N ASP A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.882A pdb=" N LEU A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 345 through 358 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 396 through 409 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 414 through 425 removed outlier: 3.548A pdb=" N LYS A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N VAL A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLY A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE A 422 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 440 Processing helix chain 'A' and resid 444 through 452 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 485 through 499 Processing helix chain 'A' and resid 499 through 505 removed outlier: 4.119A pdb=" N SER A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLN A 505 " --> pdb=" O PRO A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 776 through 783 removed outlier: 4.321A pdb=" N ILE A 780 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS A 781 " --> pdb=" O GLU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 851 removed outlier: 4.093A pdb=" N GLN A 851 " --> pdb=" O ALA A 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.598A pdb=" N VAL B 24 " --> pdb=" O HIS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 40 Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 80 through 97 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 118 through 131 removed outlier: 3.919A pdb=" N ALA B 123 " --> pdb=" O ASP B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 Processing helix chain 'B' and resid 159 through 175 Processing helix chain 'B' and resid 188 through 201 removed outlier: 3.988A pdb=" N HIS B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 232 Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.576A pdb=" N ILE B 250 " --> pdb=" O GLU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 271 Processing helix chain 'B' and resid 281 through 287 Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.839A pdb=" N LEU B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 4.219A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 358 Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 396 through 409 Proline residue: B 405 - end of helix removed outlier: 4.001A pdb=" N ASN B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 424 removed outlier: 4.094A pdb=" N VAL B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLY B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 422 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 439 Processing helix chain 'B' and resid 444 through 452 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 542 through 549 removed outlier: 4.340A pdb=" N PHE B 546 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 670 removed outlier: 4.328A pdb=" N GLY B 668 " --> pdb=" O PRO B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 783 removed outlier: 4.102A pdb=" N ILE B 780 " --> pdb=" O THR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 851 Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.928A pdb=" N MET B 932 " --> pdb=" O LEU B 929 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 933 " --> pdb=" O SER B 930 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN B 934 " --> pdb=" O HIS B 931 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 929 through 934' Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.819A pdb=" N VAL C 24 " --> pdb=" O HIS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 55 through 65 removed outlier: 3.635A pdb=" N GLY C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C 65 " --> pdb=" O LYS C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 80 through 98 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 159 through 177 removed outlier: 3.720A pdb=" N VAL C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 3.879A pdb=" N HIS C 192 " --> pdb=" O GLY C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 232 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.790A pdb=" N ILE C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 271 Processing helix chain 'C' and resid 281 through 287 Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.967A pdb=" N LEU C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 333 Processing helix chain 'C' and resid 345 through 358 Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 381 through 392 Processing helix chain 'C' and resid 396 through 410 Proline residue: C 405 - end of helix Processing helix chain 'C' and resid 414 through 424 removed outlier: 3.921A pdb=" N VAL C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE C 422 " --> pdb=" O LEU C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 439 Processing helix chain 'C' and resid 444 through 453 Processing helix chain 'C' and resid 459 through 470 Processing helix chain 'C' and resid 485 through 499 Processing helix chain 'C' and resid 499 through 504 removed outlier: 4.013A pdb=" N SER C 504 " --> pdb=" O LYS C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 622 through 626 removed outlier: 4.550A pdb=" N ASN C 625 " --> pdb=" O CYS C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 670 removed outlier: 4.457A pdb=" N ASN C 669 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C 670 " --> pdb=" O SER C 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 665 through 670' Processing helix chain 'C' and resid 747 through 751 Processing helix chain 'C' and resid 776 through 783 Processing helix chain 'C' and resid 841 through 851 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 27 through 40 Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 80 through 97 Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.531A pdb=" N VAL D 113 " --> pdb=" O ASP D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 129 removed outlier: 3.611A pdb=" N ALA D 123 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 149 Processing helix chain 'D' and resid 159 through 175 Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.931A pdb=" N HIS D 192 " --> pdb=" O GLY D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 232 Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 245 through 251 Processing helix chain 'D' and resid 254 through 271 Processing helix chain 'D' and resid 281 through 287 Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.764A pdb=" N LEU D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 removed outlier: 4.203A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 Processing helix chain 'D' and resid 367 through 379 Processing helix chain 'D' and resid 381 through 392 Processing helix chain 'D' and resid 396 through 408 Proline residue: D 405 - end of helix Processing helix chain 'D' and resid 414 through 424 removed outlier: 3.521A pdb=" N LEU D 418 " --> pdb=" O ILE D 414 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER D 424 " --> pdb=" O VAL D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 440 Processing helix chain 'D' and resid 444 through 452 Processing helix chain 'D' and resid 458 through 469 Processing helix chain 'D' and resid 485 through 499 Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 509 through 519 Processing helix chain 'D' and resid 542 through 549 removed outlier: 4.177A pdb=" N PHE D 546 " --> pdb=" O SER D 542 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU D 547 " --> pdb=" O PRO D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 removed outlier: 4.139A pdb=" N ASN D 669 " --> pdb=" O SER D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 776 through 783 Processing helix chain 'D' and resid 841 through 851 Processing helix chain 'P' and resid 43 through 54 removed outlier: 4.168A pdb=" N CYS P 50 " --> pdb=" O ARG P 46 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU P 51 " --> pdb=" O CYS P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.635A pdb=" N PHE P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU P 91 " --> pdb=" O ILE P 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'Q' and resid 65 through 67 Processing sheet with id=AA3, first strand: chain 'R' and resid 77 through 79 removed outlier: 4.258A pdb=" N PHE R 77 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE R 34 " --> pdb=" O PHE R 77 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE R 33 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR R 105 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR R 103 " --> pdb=" O THR R 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 65 through 67 Processing sheet with id=AA5, first strand: chain 'S' and resid 60 through 67 removed outlier: 7.267A pdb=" N LYS S 76 " --> pdb=" O THR S 63 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE S 65 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ILE S 74 " --> pdb=" O ILE S 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 13 through 15 removed outlier: 9.071A pdb=" N TYR A 13 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA A 69 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N VAL A 15 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N VAL A 71 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG A 67 " --> pdb=" O ILE A 100 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N MET A 102 " --> pdb=" O ARG A 67 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA A 69 " --> pdb=" O MET A 102 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL A 104 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 71 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 241 removed outlier: 6.973A pdb=" N HIS A 237 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ILE A 295 " --> pdb=" O HIS A 237 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N CYS A 239 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP A 297 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 241 " --> pdb=" O ASP A 297 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL A 299 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL A 292 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE A 321 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 294 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR A 323 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU A 296 " --> pdb=" O THR A 323 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP A 337 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 472 through 475 Processing sheet with id=AA9, first strand: chain 'A' and resid 506 through 507 removed outlier: 6.727A pdb=" N LEU A 555 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE A 629 " --> pdb=" O TYR A 653 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AB2, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AB3, first strand: chain 'A' and resid 856 through 859 Processing sheet with id=AB4, first strand: chain 'B' and resid 15 through 19 removed outlier: 3.623A pdb=" N MET B 102 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 237 through 241 removed outlier: 6.643A pdb=" N HIS B 237 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE B 295 " --> pdb=" O HIS B 237 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS B 239 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET B 209 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N TYR B 339 " --> pdb=" O MET B 209 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLY B 211 " --> pdb=" O TYR B 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 473 through 475 Processing sheet with id=AB7, first strand: chain 'B' and resid 506 through 507 removed outlier: 5.880A pdb=" N VAL B 529 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 539 through 540 removed outlier: 6.559A pdb=" N LEU B 539 " --> pdb=" O ASP B 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 605 through 606 Processing sheet with id=AC1, first strand: chain 'B' and resid 719 through 721 removed outlier: 6.302A pdb=" N ILE B 743 " --> pdb=" O ASN B 766 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 872 through 874 Processing sheet with id=AC3, first strand: chain 'C' and resid 13 through 16 removed outlier: 6.870A pdb=" N ASN C 14 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 71 through 73 removed outlier: 6.486A pdb=" N VAL C 71 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 208 through 212 removed outlier: 5.856A pdb=" N VAL C 292 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE C 321 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE C 294 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR C 323 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 296 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N HIS C 237 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE C 295 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N CYS C 239 " --> pdb=" O ILE C 295 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 473 through 475 Processing sheet with id=AC7, first strand: chain 'C' and resid 506 through 507 removed outlier: 7.108A pdb=" N LEU C 507 " --> pdb=" O SER C 530 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASP C 532 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL C 529 " --> pdb=" O LYS C 556 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N TYR C 558 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE C 531 " --> pdb=" O TYR C 558 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 700 through 701 removed outlier: 6.893A pdb=" N ILE C 743 " --> pdb=" O ASN C 766 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 879 through 880 removed outlier: 3.611A pdb=" N ILE C 880 " --> pdb=" O ILE C 971 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET C 972 " --> pdb=" O THR C 914 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR C 911 " --> pdb=" O LYS C 925 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 946 through 950 Processing sheet with id=AD2, first strand: chain 'D' and resid 237 through 241 removed outlier: 6.664A pdb=" N HIS D 237 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE D 295 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS D 239 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP D 297 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL D 241 " --> pdb=" O ASP D 297 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL D 299 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N VAL D 292 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE D 321 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE D 294 " --> pdb=" O ILE D 321 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N THR D 323 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 296 " --> pdb=" O THR D 323 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N TYR D 339 " --> pdb=" O MET D 209 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY D 211 " --> pdb=" O TYR D 339 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 474 through 475 Processing sheet with id=AD4, first strand: chain 'D' and resid 506 through 507 removed outlier: 5.894A pdb=" N VAL D 529 " --> pdb=" O LYS D 556 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TYR D 558 " --> pdb=" O VAL D 529 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE D 531 " --> pdb=" O TYR D 558 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 539 through 540 removed outlier: 4.342A pdb=" N ASP D 570 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 605 through 606 removed outlier: 6.640A pdb=" N VAL D 606 " --> pdb=" O ASP D 630 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU D 652 " --> pdb=" O MET D 677 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 742 through 744 Processing sheet with id=AD8, first strand: chain 'D' and resid 858 through 860 removed outlier: 3.852A pdb=" N LEU D 947 " --> pdb=" O LEU D 860 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 871 through 873 Processing sheet with id=AE1, first strand: chain 'P' and resid 62 through 68 removed outlier: 7.545A pdb=" N LEU P 62 " --> pdb=" O GLN P 78 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLN P 78 " --> pdb=" O LEU P 62 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER P 64 " --> pdb=" O LYS P 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS P 76 " --> pdb=" O SER P 64 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE P 72 " --> pdb=" O ASN P 68 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA P 75 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL P 36 " --> pdb=" O ALA P 75 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY P 81 " --> pdb=" O GLN P 30 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN P 30 " --> pdb=" O GLY P 81 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU P 37 " --> pdb=" O SER P 101 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N SER P 101 " --> pdb=" O GLU P 37 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2979 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10899 1.34 - 1.46: 6450 1.46 - 1.58: 16402 1.58 - 1.70: 12 1.70 - 1.82: 280 Bond restraints: 34043 Sorted by residual: bond pdb=" N ASN D 934 " pdb=" CA ASN D 934 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.29e-02 6.01e+03 1.61e+01 bond pdb=" CA ASN D 934 " pdb=" CB ASN D 934 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.69e-02 3.50e+03 4.73e+00 bond pdb=" CB MET A 491 " pdb=" CG MET A 491 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.24e+00 bond pdb=" CA PHE D 933 " pdb=" C PHE D 933 " ideal model delta sigma weight residual 1.519 1.535 -0.016 1.01e-02 9.80e+03 2.52e+00 bond pdb=" C4 ADP C1301 " pdb=" C5 ADP C1301 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.69e+00 ... (remaining 34038 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 45683 2.94 - 5.88: 333 5.88 - 8.82: 32 8.82 - 11.77: 7 11.77 - 14.71: 2 Bond angle restraints: 46057 Sorted by residual: angle pdb=" C GLN A 741 " pdb=" CA GLN A 741 " pdb=" CB GLN A 741 " ideal model delta sigma weight residual 116.54 109.81 6.73 1.15e+00 7.56e-01 3.43e+01 angle pdb=" N VAL D 854 " pdb=" CA VAL D 854 " pdb=" C VAL D 854 " ideal model delta sigma weight residual 113.71 108.23 5.48 9.50e-01 1.11e+00 3.33e+01 angle pdb=" C ARG P 94 " pdb=" N HIS P 95 " pdb=" CA HIS P 95 " ideal model delta sigma weight residual 122.11 113.89 8.22 1.59e+00 3.96e-01 2.67e+01 angle pdb=" C PHE D 933 " pdb=" N ASN D 934 " pdb=" CA ASN D 934 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 angle pdb=" CA MET A 677 " pdb=" CB MET A 677 " pdb=" CG MET A 677 " ideal model delta sigma weight residual 114.10 123.66 -9.56 2.00e+00 2.50e-01 2.28e+01 ... (remaining 46052 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.81: 19745 34.81 - 69.63: 826 69.63 - 104.44: 58 104.44 - 139.26: 2 139.26 - 174.07: 1 Dihedral angle restraints: 20632 sinusoidal: 8374 harmonic: 12258 Sorted by residual: dihedral pdb=" C2' ADP A1301 " pdb=" C1' ADP A1301 " pdb=" N9 ADP A1301 " pdb=" C4 ADP A1301 " ideal model delta sinusoidal sigma weight residual 91.55 -94.38 -174.07 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CB CYS Q 47 " pdb=" SG CYS Q 47 " pdb=" SG CYS Q 99 " pdb=" CB CYS Q 99 " ideal model delta sinusoidal sigma weight residual 93.00 144.69 -51.69 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CB CYS R 47 " pdb=" SG CYS R 47 " pdb=" SG CYS R 99 " pdb=" CB CYS R 99 " ideal model delta sinusoidal sigma weight residual 93.00 144.15 -51.15 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 20629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3932 0.046 - 0.092: 1049 0.092 - 0.138: 281 0.138 - 0.184: 21 0.184 - 0.230: 3 Chirality restraints: 5286 Sorted by residual: chirality pdb=" CB ILE B 743 " pdb=" CA ILE B 743 " pdb=" CG1 ILE B 743 " pdb=" CG2 ILE B 743 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE C 90 " pdb=" CA ILE C 90 " pdb=" CG1 ILE C 90 " pdb=" CG2 ILE C 90 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE A 90 " pdb=" CA ILE A 90 " pdb=" CG1 ILE A 90 " pdb=" CG2 ILE A 90 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.81e-01 ... (remaining 5283 not shown) Planarity restraints: 5831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 99 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.11e+00 pdb=" CD GLN A 99 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLN A 99 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 GLN A 99 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 579 " -0.177 9.50e-02 1.11e+02 7.99e-02 4.84e+00 pdb=" NE ARG B 579 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 579 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG B 579 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG B 579 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 21 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO C 22 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 22 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 22 " -0.029 5.00e-02 4.00e+02 ... (remaining 5828 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 15497 2.95 - 3.43: 35278 3.43 - 3.92: 57131 3.92 - 4.41: 65943 4.41 - 4.90: 106307 Nonbonded interactions: 280156 Sorted by model distance: nonbonded pdb=" O ASP C 475 " pdb=" CA LYS C 480 " model vdw 2.457 2.776 nonbonded pdb=" O2' ADP B1301 " pdb=" O3' ADP B1301 " model vdw 2.467 2.432 nonbonded pdb=" O2' ADP D1301 " pdb=" O3' ADP D1301 " model vdw 2.472 2.432 nonbonded pdb=" N SER D 937 " pdb=" O GLN P 96 " model vdw 2.496 3.120 nonbonded pdb=" O2' ADP C1301 " pdb=" O3' ADP C1301 " model vdw 2.505 2.432 ... (remaining 280151 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 'A' selection = (chain 'B' and resid 11 through 1301) selection = chain 'C' selection = (chain 'D' and resid 11 through 1301) } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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=0.00 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: 4.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 31.940 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 34053 Z= 0.178 Angle : 0.676 14.706 46077 Z= 0.354 Chirality : 0.044 0.230 5286 Planarity : 0.004 0.080 5831 Dihedral : 18.189 174.069 12622 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.21 % Favored : 90.47 % Rotamer: Outliers : 4.01 % Allowed : 28.51 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.13), residues: 4178 helix: 1.01 (0.14), residues: 1349 sheet: -2.31 (0.24), residues: 435 loop : -2.06 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG B 579 TYR 0.015 0.001 TYR A 755 PHE 0.028 0.001 PHE A 698 TRP 0.032 0.001 TRP A 774 HIS 0.012 0.001 HIS P 95 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (34043) covalent geometry : angle 0.67606 / 0.35 (46057) SS BOND : bond 0.00166 / 0.10 ( 10) SS BOND : angle 0.79561 / 0.51 ( 20) hydrogen bonds : bond 0.08746 / 6.21 ( 1025) hydrogen bonds : angle 5.51896 / 3.96 ( 2979) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 472 time to evaluate : 1.277 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 85 ASP cc_start: 0.7707 (m-30) cc_final: 0.7325 (m-30) REVERT: A 135 GLU cc_start: 0.7386 (tp30) cc_final: 0.7186 (tp30) REVERT: A 311 MET cc_start: 0.7142 (tpp) cc_final: 0.6518 (mmm) REVERT: A 513 ILE cc_start: 0.8034 (mp) cc_final: 0.7675 (mp) REVERT: A 710 PHE cc_start: 0.6684 (t80) cc_final: 0.6444 (t80) REVERT: A 825 LEU cc_start: 0.2516 (OUTLIER) cc_final: 0.2286 (pp) REVERT: A 894 MET cc_start: 0.5857 (mmp) cc_final: 0.5551 (mmt) REVERT: A 911 TYR cc_start: 0.2898 (OUTLIER) cc_final: 0.1918 (m-80) REVERT: B 60 LYS cc_start: 0.7195 (tptt) cc_final: 0.6990 (mptt) REVERT: B 83 CYS cc_start: 0.8359 (m) cc_final: 0.8046 (m) REVERT: B 451 MET cc_start: 0.8091 (mmp) cc_final: 0.7699 (mmt) REVERT: B 589 TYR cc_start: 0.7890 (t80) cc_final: 0.7348 (t80) REVERT: B 625 ASN cc_start: 0.8298 (m-40) cc_final: 0.7968 (t0) REVERT: B 710 PHE cc_start: 0.5899 (t80) cc_final: 0.5440 (t80) REVERT: B 825 LEU cc_start: 0.0554 (OUTLIER) cc_final: -0.0211 (tp) REVERT: B 894 MET cc_start: 0.0658 (mmm) cc_final: -0.0644 (tpp) REVERT: C 134 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7489 (mp0) REVERT: C 136 ARG cc_start: 0.7545 (ttm170) cc_final: 0.7016 (mtm-85) REVERT: C 263 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6976 (tm-30) REVERT: C 649 LEU cc_start: 0.5692 (tp) cc_final: 0.5477 (tp) REVERT: C 761 SER cc_start: 0.7303 (OUTLIER) cc_final: 0.6893 (p) REVERT: C 818 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5783 (mp) REVERT: C 894 MET cc_start: 0.5164 (tpp) cc_final: 0.4737 (tpp) REVERT: C 932 MET cc_start: -0.0694 (OUTLIER) cc_final: -0.1152 (ppp) REVERT: C 972 MET cc_start: 0.7184 (mmp) cc_final: 0.6752 (tpp) REVERT: D 126 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7257 (tp30) REVERT: D 323 THR cc_start: 0.8541 (m) cc_final: 0.8049 (p) REVERT: D 566 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.6754 (tptp) REVERT: D 639 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5617 (pm20) REVERT: D 774 TRP cc_start: 0.6676 (t60) cc_final: 0.6031 (t60) REVERT: D 857 TRP cc_start: 0.5350 (p-90) cc_final: 0.5137 (p-90) REVERT: D 932 MET cc_start: 0.4207 (OUTLIER) cc_final: 0.3793 (tpp) REVERT: D 933 PHE cc_start: 0.4446 (OUTLIER) cc_final: 0.3759 (m-80) outliers start: 151 outliers final: 62 residues processed: 598 average time/residue: 0.1989 time to fit residues: 198.0222 Evaluate side-chains 358 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 285 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 834 PHE Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 911 TYR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 952 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 622 CYS Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 879 ILE Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 9 ARG Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 639 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 765 ILE Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 933 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 96 GLN A 39 ASN A 99 GLN A 238 ASN A 331 GLN A 736 HIS A 836 ASN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 238 ASN B 264 GLN B 279 HIS C 34 GLN C 238 ASN C 247 ASN ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN P 96 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.146588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.099452 restraints weight = 76937.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098921 restraints weight = 50172.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.098728 restraints weight = 36230.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.099170 restraints weight = 34388.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.099538 restraints weight = 30576.586| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 34053 Z= 0.140 Angle : 0.646 12.508 46077 Z= 0.320 Chirality : 0.044 0.231 5286 Planarity : 0.004 0.048 5831 Dihedral : 7.954 167.737 4633 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.64 % Favored : 91.05 % Rotamer: Outliers : 4.88 % Allowed : 27.51 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4178 helix: 1.06 (0.14), residues: 1367 sheet: -2.42 (0.25), residues: 414 loop : -1.99 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 872 TYR 0.017 0.002 TYR C 833 PHE 0.032 0.002 PHE A 265 TRP 0.024 0.001 TRP B 586 HIS 0.014 0.001 HIS C 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (34043) covalent geometry : angle 0.64552 / 0.32 (46057) SS BOND : bond 0.00198 / 0.12 ( 10) SS BOND : angle 0.80468 / 0.50 ( 20) hydrogen bonds : bond 0.03354 / 2.35 ( 1025) hydrogen bonds : angle 5.11243 / 3.66 ( 2979) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 327 time to evaluate : 1.434 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: S 40 HIS cc_start: 0.2417 (p-80) cc_final: 0.1868 (p-80) REVERT: A 135 GLU cc_start: 0.7563 (tp30) cc_final: 0.7317 (tp30) REVERT: A 491 MET cc_start: 0.8082 (tmm) cc_final: 0.7796 (tmm) REVERT: A 513 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7887 (mp) REVERT: A 556 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6896 (tttm) REVERT: A 673 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5063 (tt) REVERT: A 677 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6672 (mmp) REVERT: A 678 MET cc_start: 0.7164 (tpp) cc_final: 0.6912 (tpp) REVERT: A 710 PHE cc_start: 0.6547 (t80) cc_final: 0.6282 (t80) REVERT: A 745 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7187 (mm) REVERT: A 808 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7271 (mttm) REVERT: A 818 LEU cc_start: 0.4785 (OUTLIER) cc_final: 0.4567 (tt) REVERT: A 894 MET cc_start: 0.5799 (mmp) cc_final: 0.5535 (mmp) REVERT: A 911 TYR cc_start: 0.2839 (OUTLIER) cc_final: 0.1885 (m-80) REVERT: B 83 CYS cc_start: 0.8389 (m) cc_final: 0.8093 (m) REVERT: B 451 MET cc_start: 0.8162 (mmp) cc_final: 0.7895 (mmt) REVERT: B 589 TYR cc_start: 0.7580 (t80) cc_final: 0.6789 (t80) REVERT: B 608 MET cc_start: 0.7795 (ttm) cc_final: 0.7248 (ttm) REVERT: B 625 ASN cc_start: 0.8228 (m-40) cc_final: 0.7947 (t0) REVERT: B 825 LEU cc_start: 0.0817 (OUTLIER) cc_final: -0.0001 (tp) REVERT: B 894 MET cc_start: 0.0247 (mmm) cc_final: -0.0917 (tpp) REVERT: B 932 MET cc_start: 0.3906 (OUTLIER) cc_final: 0.3529 (ptp) REVERT: C 134 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7569 (mp0) REVERT: C 136 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7261 (mtm-85) REVERT: C 209 MET cc_start: 0.6621 (ptp) cc_final: 0.6406 (ptm) REVERT: C 263 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: C 548 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8085 (mtpt) REVERT: C 698 PHE cc_start: 0.4407 (OUTLIER) cc_final: 0.3774 (t80) REVERT: C 714 PRO cc_start: 0.6257 (Cg_endo) cc_final: 0.5916 (Cg_exo) REVERT: C 744 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6503 (mmmm) REVERT: C 809 ILE cc_start: 0.5153 (OUTLIER) cc_final: 0.4430 (mm) REVERT: C 833 TYR cc_start: 0.6269 (m-10) cc_final: 0.5222 (m-80) REVERT: C 896 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4915 (tt) REVERT: C 932 MET cc_start: -0.0363 (OUTLIER) cc_final: -0.0651 (ppp) REVERT: C 972 MET cc_start: 0.7281 (mmp) cc_final: 0.6837 (tpp) REVERT: D 96 TYR cc_start: 0.6722 (t80) cc_final: 0.6419 (m-10) REVERT: D 424 SER cc_start: 0.9046 (OUTLIER) cc_final: 0.8840 (t) REVERT: D 530 SER cc_start: 0.7779 (OUTLIER) cc_final: 0.7225 (p) REVERT: D 540 MET cc_start: 0.7363 (tpt) cc_final: 0.7073 (tpt) REVERT: D 566 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7053 (tptp) REVERT: D 677 MET cc_start: 0.6299 (mmp) cc_final: 0.5992 (mmp) REVERT: D 774 TRP cc_start: 0.6773 (t60) cc_final: 0.6154 (t60) REVERT: D 857 TRP cc_start: 0.5172 (p-90) cc_final: 0.4846 (p-90) REVERT: D 907 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.3628 (tpp-160) REVERT: D 933 PHE cc_start: 0.4409 (OUTLIER) cc_final: 0.3654 (m-80) REVERT: D 975 PHE cc_start: -0.0022 (OUTLIER) cc_final: -0.0672 (m-80) REVERT: D 986 GLU cc_start: 0.4133 (OUTLIER) cc_final: 0.3000 (pm20) REVERT: D 987 CYS cc_start: -0.0574 (OUTLIER) cc_final: -0.1104 (m) outliers start: 184 outliers final: 71 residues processed: 485 average time/residue: 0.2069 time to fit residues: 167.8441 Evaluate side-chains 366 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 271 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 834 PHE Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 911 TYR Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 684 LEU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 546 PHE Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 744 LYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 424 SER Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 852 SER Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 907 ARG Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 986 GLU Chi-restraints excluded: chain D residue 987 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 26 optimal weight: 5.9990 chunk 237 optimal weight: 6.9990 chunk 395 optimal weight: 5.9990 chunk 366 optimal weight: 7.9990 chunk 415 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 399 optimal weight: 30.0000 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 352 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 99 GLN A 238 ASN A 331 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 238 ASN B 247 ASN B 333 HIS B 447 HIS B 499 GLN B 721 GLN C 237 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 GLN C 585 HIS C 824 HIS ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 279 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN D 931 HIS ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.142220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091146 restraints weight = 77764.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092759 restraints weight = 46203.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.093332 restraints weight = 32515.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.093936 restraints weight = 26111.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.094338 restraints weight = 24493.543| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 34053 Z= 0.330 Angle : 0.835 11.169 46077 Z= 0.424 Chirality : 0.051 0.330 5286 Planarity : 0.006 0.086 5831 Dihedral : 8.328 173.634 4576 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.34 % Allowed : 10.70 % Favored : 88.97 % Rotamer: Outliers : 6.82 % Allowed : 26.82 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.12), residues: 4178 helix: 0.33 (0.14), residues: 1350 sheet: -2.59 (0.24), residues: 431 loop : -2.24 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 169 TYR 0.025 0.003 TYR D 77 PHE 0.034 0.003 PHE A 265 TRP 0.023 0.002 TRP D 617 HIS 0.011 0.002 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.33 (34043) covalent geometry : angle 0.83538 / 0.42 (46057) SS BOND : bond 0.00166 / 0.09 ( 10) SS BOND : angle 0.76634 / 0.50 ( 20) hydrogen bonds : bond 0.05326 / 3.73 ( 1025) hydrogen bonds : angle 5.58714 / 3.97 ( 2979) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 257 poor density : 265 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7968 (tp30) cc_final: 0.7611 (tp30) REVERT: A 136 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7656 (ttm170) REVERT: A 548 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8355 (mtpt) REVERT: A 549 MET cc_start: 0.8434 (tpp) cc_final: 0.7988 (mmt) REVERT: A 736 HIS cc_start: 0.5433 (OUTLIER) cc_final: 0.4708 (p90) REVERT: A 765 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7494 (mm) REVERT: A 818 LEU cc_start: 0.5050 (OUTLIER) cc_final: 0.4832 (tt) REVERT: A 834 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7576 (t80) REVERT: A 894 MET cc_start: 0.5836 (mmp) cc_final: 0.5414 (mmt) REVERT: B 60 LYS cc_start: 0.6616 (mptt) cc_final: 0.6149 (tptt) REVERT: B 158 LYS cc_start: 0.8787 (tppt) cc_final: 0.8036 (tmtt) REVERT: B 356 SER cc_start: 0.9104 (m) cc_final: 0.8806 (t) REVERT: B 428 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7933 (mtpm) REVERT: B 623 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7026 (pp) REVERT: B 677 MET cc_start: 0.5294 (mmp) cc_final: 0.5032 (mmp) REVERT: B 825 LEU cc_start: 0.0435 (OUTLIER) cc_final: -0.0316 (tp) REVERT: B 840 LEU cc_start: 0.3599 (OUTLIER) cc_final: 0.3215 (tp) REVERT: B 894 MET cc_start: 0.0899 (mmm) cc_final: -0.0286 (tpp) REVERT: B 932 MET cc_start: 0.4036 (OUTLIER) cc_final: 0.3669 (ptp) REVERT: C 84 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8591 (mm) REVERT: C 135 GLU cc_start: 0.7507 (tp30) cc_final: 0.7287 (tp30) REVERT: C 136 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7399 (mtt90) REVERT: C 263 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: C 491 MET cc_start: 0.8149 (ttp) cc_final: 0.7942 (tmm) REVERT: C 548 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8419 (mtpt) REVERT: C 677 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5941 (mmm) REVERT: C 683 SER cc_start: 0.5158 (OUTLIER) cc_final: 0.4693 (p) REVERT: C 685 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5516 (pm20) REVERT: C 698 PHE cc_start: 0.5068 (OUTLIER) cc_final: 0.4447 (t80) REVERT: C 741 GLN cc_start: 0.6030 (mm110) cc_final: 0.4968 (tt0) REVERT: C 809 ILE cc_start: 0.5244 (OUTLIER) cc_final: 0.4297 (mm) REVERT: C 833 TYR cc_start: 0.6432 (m-10) cc_final: 0.5586 (m-80) REVERT: C 871 HIS cc_start: 0.4668 (t-90) cc_final: 0.2919 (m90) REVERT: C 972 MET cc_start: 0.7178 (mmp) cc_final: 0.6726 (tpp) REVERT: D 53 GLN cc_start: 0.7399 (tp40) cc_final: 0.7013 (tp-100) REVERT: D 102 MET cc_start: 0.8153 (mtt) cc_final: 0.7554 (mtt) REVERT: D 103 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8039 (p) REVERT: D 530 SER cc_start: 0.8509 (OUTLIER) cc_final: 0.7832 (p) REVERT: D 551 ASN cc_start: 0.7213 (m-40) cc_final: 0.7010 (m-40) REVERT: D 566 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.6870 (tptp) REVERT: D 677 MET cc_start: 0.5883 (mmp) cc_final: 0.5393 (mmp) REVERT: D 774 TRP cc_start: 0.6970 (t60) cc_final: 0.6335 (t60) REVERT: D 907 ARG cc_start: 0.5075 (OUTLIER) cc_final: 0.3921 (tpp-160) REVERT: D 932 MET cc_start: 0.2935 (mmt) cc_final: 0.2458 (mmp) REVERT: D 975 PHE cc_start: 0.0325 (OUTLIER) cc_final: 0.0035 (m-80) outliers start: 257 outliers final: 139 residues processed: 487 average time/residue: 0.2022 time to fit residues: 166.3068 Evaluate side-chains 388 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 227 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 496 CYS Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 622 CYS Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 736 HIS Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 834 PHE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 440 PHE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 649 LEU Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 818 LEU Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 826 ASN Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 689 SER Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 765 ILE Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 852 SER Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 907 ARG Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 327 optimal weight: 0.9990 chunk 318 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 chunk 252 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 311 optimal weight: 30.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 333 HIS A 607 ASN A 614 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.143779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.095077 restraints weight = 76606.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.094321 restraints weight = 50344.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.094893 restraints weight = 35698.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.095825 restraints weight = 31230.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.096013 restraints weight = 28182.692| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 34053 Z= 0.156 Angle : 0.632 12.149 46077 Z= 0.317 Chirality : 0.044 0.215 5286 Planarity : 0.004 0.054 5831 Dihedral : 7.745 179.769 4565 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.43 % Favored : 91.29 % Rotamer: Outliers : 4.69 % Allowed : 28.81 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.13), residues: 4178 helix: 0.87 (0.14), residues: 1346 sheet: -2.40 (0.25), residues: 426 loop : -2.14 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 907 TYR 0.020 0.001 TYR C 515 PHE 0.027 0.001 PHE A 265 TRP 0.019 0.001 TRP B 774 HIS 0.004 0.001 HIS D 931 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (34043) covalent geometry : angle 0.63207 / 0.32 (46057) SS BOND : bond 0.00153 / 0.08 ( 10) SS BOND : angle 0.67455 / 0.42 ( 20) hydrogen bonds : bond 0.03672 / 2.57 ( 1025) hydrogen bonds : angle 5.08370 / 3.62 ( 2979) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 243 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7867 (tp30) cc_final: 0.7354 (tp30) REVERT: A 136 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7781 (ttm170) REVERT: A 232 SER cc_start: 0.8493 (OUTLIER) cc_final: 0.8262 (p) REVERT: A 548 LYS cc_start: 0.8548 (mmmm) cc_final: 0.8260 (mtpt) REVERT: A 573 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: A 631 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6839 (pp) REVERT: A 673 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.6017 (tt) REVERT: B 60 LYS cc_start: 0.6393 (mptt) cc_final: 0.6121 (mptt) REVERT: B 158 LYS cc_start: 0.8805 (tppt) cc_final: 0.8050 (tmtt) REVERT: B 623 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7041 (pp) REVERT: B 825 LEU cc_start: 0.0734 (OUTLIER) cc_final: -0.0082 (tp) REVERT: B 833 TYR cc_start: 0.6556 (m-80) cc_final: 0.6223 (m-80) REVERT: B 840 LEU cc_start: 0.3708 (OUTLIER) cc_final: 0.3319 (tp) REVERT: B 894 MET cc_start: 0.0715 (mmm) cc_final: -0.0405 (tpp) REVERT: B 932 MET cc_start: 0.3861 (OUTLIER) cc_final: 0.3422 (ptp) REVERT: C 84 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8546 (mm) REVERT: C 136 ARG cc_start: 0.8143 (ttm170) cc_final: 0.7583 (mtt90) REVERT: C 163 MET cc_start: 0.8478 (tmm) cc_final: 0.8061 (ttt) REVERT: C 451 MET cc_start: 0.8734 (mtp) cc_final: 0.8092 (mmt) REVERT: C 698 PHE cc_start: 0.4918 (OUTLIER) cc_final: 0.4246 (t80) REVERT: C 741 GLN cc_start: 0.5966 (mm110) cc_final: 0.4961 (tt0) REVERT: C 809 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.4554 (mm) REVERT: C 833 TYR cc_start: 0.6187 (m-10) cc_final: 0.5274 (m-80) REVERT: C 894 MET cc_start: 0.6119 (tpp) cc_final: 0.5773 (tpp) REVERT: C 896 LEU cc_start: 0.4896 (OUTLIER) cc_final: 0.4513 (tt) REVERT: C 900 GLN cc_start: 0.4636 (OUTLIER) cc_final: 0.4429 (tm-30) REVERT: C 910 LEU cc_start: 0.6756 (OUTLIER) cc_final: 0.6166 (tp) REVERT: C 932 MET cc_start: -0.0464 (OUTLIER) cc_final: -0.0841 (ppp) REVERT: D 53 GLN cc_start: 0.7192 (tp40) cc_final: 0.6792 (tp40) REVERT: D 60 LYS cc_start: 0.8069 (tptt) cc_final: 0.7809 (mttt) REVERT: D 103 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7877 (p) REVERT: D 491 MET cc_start: 0.7592 (tmm) cc_final: 0.7234 (ttp) REVERT: D 530 SER cc_start: 0.8501 (OUTLIER) cc_final: 0.7856 (p) REVERT: D 551 ASN cc_start: 0.7542 (m-40) cc_final: 0.7278 (m-40) REVERT: D 566 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.6922 (tptp) REVERT: D 774 TRP cc_start: 0.6940 (t60) cc_final: 0.6283 (t60) REVERT: D 932 MET cc_start: 0.2855 (mmt) cc_final: 0.1729 (mmp) REVERT: D 975 PHE cc_start: 0.0442 (OUTLIER) cc_final: 0.0185 (m-80) outliers start: 177 outliers final: 101 residues processed: 398 average time/residue: 0.2039 time to fit residues: 136.2076 Evaluate side-chains 341 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 221 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 794 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 826 ASN Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 900 GLN Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 852 SER Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 6 optimal weight: 0.9980 chunk 318 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 chunk 408 optimal weight: 3.9990 chunk 381 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 338 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 106 optimal weight: 30.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 GLN B 876 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.142492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.090800 restraints weight = 77239.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093402 restraints weight = 46198.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.093508 restraints weight = 30633.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.094214 restraints weight = 25167.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094515 restraints weight = 22929.936| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34053 Z= 0.205 Angle : 0.645 12.474 46077 Z= 0.322 Chirality : 0.044 0.196 5286 Planarity : 0.004 0.051 5831 Dihedral : 7.649 179.144 4563 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.96 % Favored : 89.80 % Rotamer: Outliers : 5.41 % Allowed : 27.75 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 4178 helix: 0.91 (0.14), residues: 1351 sheet: -2.38 (0.25), residues: 432 loop : -2.14 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 9 TYR 0.022 0.001 TYR B 515 PHE 0.023 0.002 PHE D 838 TRP 0.021 0.001 TRP B 774 HIS 0.006 0.001 HIS D 237 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (34043) covalent geometry : angle 0.64463 / 0.32 (46057) SS BOND : bond 0.00137 / 0.07 ( 10) SS BOND : angle 0.65492 / 0.42 ( 20) hydrogen bonds : bond 0.03861 / 2.68 ( 1025) hydrogen bonds : angle 5.07280 / 3.61 ( 2979) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 221 time to evaluate : 1.421 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 135 GLU cc_start: 0.7752 (tp30) cc_final: 0.7214 (tp30) REVERT: A 136 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7788 (ttm170) REVERT: A 186 MET cc_start: 0.8927 (mmt) cc_final: 0.8194 (mmm) REVERT: A 232 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8301 (p) REVERT: A 548 LYS cc_start: 0.8644 (mmmm) cc_final: 0.8407 (mtpt) REVERT: A 556 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6172 (tptm) REVERT: A 573 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7448 (mt-10) REVERT: A 631 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7044 (pp) REVERT: A 673 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6137 (tt) REVERT: A 708 ARG cc_start: 0.2370 (OUTLIER) cc_final: 0.0792 (ptp90) REVERT: A 745 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7456 (mm) REVERT: A 765 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7424 (mm) REVERT: A 772 ILE cc_start: 0.5619 (OUTLIER) cc_final: 0.5298 (mm) REVERT: A 849 ILE cc_start: 0.5011 (OUTLIER) cc_final: 0.4381 (mm) REVERT: A 869 PHE cc_start: 0.0094 (OUTLIER) cc_final: -0.0299 (m-10) REVERT: B 158 LYS cc_start: 0.8847 (tppt) cc_final: 0.7940 (tmtt) REVERT: B 410 CYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6850 (t) REVERT: B 623 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7187 (pp) REVERT: B 677 MET cc_start: 0.5349 (mmp) cc_final: 0.5120 (mmp) REVERT: B 736 HIS cc_start: 0.6241 (OUTLIER) cc_final: 0.5264 (t-90) REVERT: B 825 LEU cc_start: 0.0671 (OUTLIER) cc_final: -0.0075 (tp) REVERT: B 840 LEU cc_start: 0.3887 (OUTLIER) cc_final: 0.3411 (tp) REVERT: B 894 MET cc_start: 0.0822 (mmm) cc_final: -0.0340 (tpp) REVERT: B 932 MET cc_start: 0.3750 (OUTLIER) cc_final: 0.3397 (ptp) REVERT: B 986 GLU cc_start: 0.5256 (OUTLIER) cc_final: 0.4820 (pp20) REVERT: C 33 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7682 (mtm110) REVERT: C 136 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7466 (ttm-80) REVERT: C 451 MET cc_start: 0.8786 (mtp) cc_final: 0.8171 (mmt) REVERT: C 683 SER cc_start: 0.5223 (OUTLIER) cc_final: 0.4697 (p) REVERT: C 685 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5697 (pm20) REVERT: C 698 PHE cc_start: 0.4968 (OUTLIER) cc_final: 0.4334 (t80) REVERT: C 741 GLN cc_start: 0.6038 (mm110) cc_final: 0.4932 (tt0) REVERT: C 809 ILE cc_start: 0.5743 (OUTLIER) cc_final: 0.4896 (mm) REVERT: C 833 TYR cc_start: 0.6491 (m-10) cc_final: 0.5604 (m-80) REVERT: C 871 HIS cc_start: 0.4652 (t-90) cc_final: 0.2693 (m90) REVERT: C 894 MET cc_start: 0.6261 (tpp) cc_final: 0.5967 (tpp) REVERT: C 896 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4817 (tt) REVERT: C 910 LEU cc_start: 0.6948 (OUTLIER) cc_final: 0.6352 (tp) REVERT: C 932 MET cc_start: -0.0418 (OUTLIER) cc_final: -0.0702 (ppp) REVERT: C 972 MET cc_start: 0.7211 (tpp) cc_final: 0.6933 (tpp) REVERT: D 53 GLN cc_start: 0.7432 (tp40) cc_final: 0.6942 (tp40) REVERT: D 103 THR cc_start: 0.8260 (OUTLIER) cc_final: 0.7957 (p) REVERT: D 491 MET cc_start: 0.7556 (tmm) cc_final: 0.7148 (ttp) REVERT: D 518 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: D 530 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.7879 (p) REVERT: D 551 ASN cc_start: 0.7541 (m-40) cc_final: 0.7326 (m-40) REVERT: D 566 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.6814 (tptp) REVERT: D 677 MET cc_start: 0.5602 (mmt) cc_final: 0.5375 (mmp) REVERT: D 774 TRP cc_start: 0.7101 (t60) cc_final: 0.6469 (t60) REVERT: D 975 PHE cc_start: 0.0385 (OUTLIER) cc_final: 0.0107 (m-80) outliers start: 204 outliers final: 126 residues processed: 405 average time/residue: 0.2018 time to fit residues: 138.6089 Evaluate side-chains 376 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 218 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 623 LEU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 794 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 986 GLU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 495 VAL Chi-restraints excluded: chain D residue 518 GLU Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 764 HIS Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 852 SER Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 931 HIS Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 57 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 312 optimal weight: 0.6980 chunk 345 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 379 optimal weight: 9.9990 chunk 364 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 736 HIS ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 ASN B 899 HIS C 238 ASN ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.143767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.092607 restraints weight = 76648.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.095291 restraints weight = 44501.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.095690 restraints weight = 26852.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.096036 restraints weight = 25079.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096315 restraints weight = 23583.390| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34053 Z= 0.139 Angle : 0.610 12.446 46077 Z= 0.302 Chirality : 0.043 0.164 5286 Planarity : 0.004 0.054 5831 Dihedral : 7.420 175.720 4561 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.38 % Favored : 91.38 % Rotamer: Outliers : 4.51 % Allowed : 28.67 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.13), residues: 4178 helix: 1.07 (0.14), residues: 1356 sheet: -2.25 (0.25), residues: 419 loop : -2.09 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 579 TYR 0.018 0.001 TYR B 515 PHE 0.020 0.001 PHE A 265 TRP 0.022 0.001 TRP B 774 HIS 0.006 0.001 HIS C 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (34043) covalent geometry : angle 0.60986 / 0.30 (46057) SS BOND : bond 0.00144 / 0.07 ( 10) SS BOND : angle 0.64491 / 0.41 ( 20) hydrogen bonds : bond 0.03375 / 2.35 ( 1025) hydrogen bonds : angle 4.92125 / 3.50 ( 2979) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 225 time to evaluate : 1.344 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 135 GLU cc_start: 0.7766 (tp30) cc_final: 0.7186 (tp30) REVERT: A 136 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7818 (ttm170) REVERT: A 186 MET cc_start: 0.8930 (mmt) cc_final: 0.8160 (mmm) REVERT: A 232 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8252 (p) REVERT: A 556 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6142 (tptm) REVERT: A 573 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: A 631 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7055 (pp) REVERT: A 703 LYS cc_start: 0.7709 (mptt) cc_final: 0.7466 (mptt) REVERT: A 708 ARG cc_start: 0.2440 (OUTLIER) cc_final: 0.0895 (ptp90) REVERT: A 765 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7394 (mm) REVERT: A 772 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5242 (mm) REVERT: A 869 PHE cc_start: 0.0212 (OUTLIER) cc_final: -0.0180 (m-10) REVERT: B 60 LYS cc_start: 0.6403 (mptt) cc_final: 0.6202 (mptt) REVERT: B 96 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.6339 (t80) REVERT: B 158 LYS cc_start: 0.8852 (tppt) cc_final: 0.8085 (tmtt) REVERT: B 410 CYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6662 (t) REVERT: B 736 HIS cc_start: 0.6264 (OUTLIER) cc_final: 0.5284 (t-90) REVERT: B 825 LEU cc_start: 0.0768 (OUTLIER) cc_final: -0.0041 (tp) REVERT: B 833 TYR cc_start: 0.6521 (m-80) cc_final: 0.6020 (m-80) REVERT: B 840 LEU cc_start: 0.4076 (OUTLIER) cc_final: 0.3573 (tp) REVERT: B 894 MET cc_start: 0.0669 (mmm) cc_final: -0.0276 (tpp) REVERT: B 932 MET cc_start: 0.3724 (OUTLIER) cc_final: 0.3357 (ptp) REVERT: B 942 LEU cc_start: 0.4893 (OUTLIER) cc_final: 0.3882 (mp) REVERT: C 136 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7719 (mtt90) REVERT: C 163 MET cc_start: 0.8524 (tmm) cc_final: 0.8091 (ttt) REVERT: C 451 MET cc_start: 0.8755 (mtp) cc_final: 0.8168 (mmt) REVERT: C 615 LYS cc_start: 0.4843 (mttm) cc_final: 0.4566 (mmtp) REVERT: C 677 MET cc_start: 0.6166 (mmt) cc_final: 0.5879 (mmm) REVERT: C 685 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5641 (pm20) REVERT: C 698 PHE cc_start: 0.4922 (OUTLIER) cc_final: 0.4603 (t80) REVERT: C 741 GLN cc_start: 0.5993 (mm110) cc_final: 0.5066 (tt0) REVERT: C 809 ILE cc_start: 0.5716 (OUTLIER) cc_final: 0.4913 (mm) REVERT: C 833 TYR cc_start: 0.6489 (m-10) cc_final: 0.5604 (m-80) REVERT: C 871 HIS cc_start: 0.4544 (t-90) cc_final: 0.2607 (m90) REVERT: C 896 LEU cc_start: 0.5012 (OUTLIER) cc_final: 0.4730 (tt) REVERT: C 910 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6412 (tp) REVERT: C 932 MET cc_start: -0.0261 (OUTLIER) cc_final: -0.0691 (ppp) REVERT: C 972 MET cc_start: 0.7329 (tpp) cc_final: 0.6865 (tpp) REVERT: D 53 GLN cc_start: 0.7314 (tp40) cc_final: 0.6856 (tp40) REVERT: D 60 LYS cc_start: 0.8068 (tptt) cc_final: 0.7721 (mttt) REVERT: D 76 ASN cc_start: 0.8170 (OUTLIER) cc_final: 0.7839 (p0) REVERT: D 103 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7881 (p) REVERT: D 491 MET cc_start: 0.7544 (tmm) cc_final: 0.7194 (ttp) REVERT: D 518 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: D 530 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.7849 (p) REVERT: D 551 ASN cc_start: 0.7681 (m-40) cc_final: 0.7461 (m-40) REVERT: D 566 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.6862 (tptp) REVERT: D 677 MET cc_start: 0.5440 (mmt) cc_final: 0.5174 (mmp) REVERT: D 774 TRP cc_start: 0.7150 (t60) cc_final: 0.6507 (t60) REVERT: D 975 PHE cc_start: 0.0372 (OUTLIER) cc_final: 0.0094 (m-80) REVERT: P 99 CYS cc_start: 0.0199 (OUTLIER) cc_final: -0.0038 (m) outliers start: 170 outliers final: 115 residues processed: 377 average time/residue: 0.1992 time to fit residues: 126.8366 Evaluate side-chains 360 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 216 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 65 ILE Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 96 TYR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 410 CYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 794 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 876 ASN Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 826 ASN Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 518 GLU Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 852 SER Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Chi-restraints excluded: chain P residue 96 GLN Chi-restraints excluded: chain P residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 382 optimal weight: 0.0670 chunk 46 optimal weight: 0.8980 chunk 330 optimal weight: 3.9990 chunk 383 optimal weight: 6.9990 chunk 306 optimal weight: 1.9990 chunk 187 optimal weight: 20.0000 chunk 259 optimal weight: 3.9990 chunk 389 optimal weight: 20.0000 chunk 205 optimal weight: 40.0000 chunk 370 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 ASN ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 ASN ** C 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 ASN ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.091141 restraints weight = 77150.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093707 restraints weight = 44330.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093750 restraints weight = 31012.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.094566 restraints weight = 25067.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.094992 restraints weight = 22481.909| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34053 Z= 0.189 Angle : 0.636 12.581 46077 Z= 0.316 Chirality : 0.044 0.168 5286 Planarity : 0.004 0.053 5831 Dihedral : 7.449 176.663 4561 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.57 % Favored : 90.19 % Rotamer: Outliers : 5.17 % Allowed : 28.46 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.13), residues: 4178 helix: 1.01 (0.14), residues: 1359 sheet: -2.17 (0.26), residues: 411 loop : -2.13 (0.12), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 9 TYR 0.018 0.001 TYR B 515 PHE 0.017 0.001 PHE A 265 TRP 0.024 0.001 TRP B 774 HIS 0.005 0.001 HIS C 333 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (34043) covalent geometry : angle 0.63586 / 0.32 (46057) SS BOND : bond 0.00136 / 0.07 ( 10) SS BOND : angle 0.65249 / 0.42 ( 20) hydrogen bonds : bond 0.03632 / 2.52 ( 1025) hydrogen bonds : angle 4.98002 / 3.55 ( 2979) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 225 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7738 (tp30) cc_final: 0.7185 (tp30) REVERT: A 136 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7796 (ttm170) REVERT: A 186 MET cc_start: 0.8938 (mmt) cc_final: 0.8184 (mmm) REVERT: A 232 SER cc_start: 0.8516 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 556 LYS cc_start: 0.7308 (OUTLIER) cc_final: 0.6147 (tptm) REVERT: A 573 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: A 631 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7193 (pp) REVERT: A 703 LYS cc_start: 0.7719 (mptt) cc_final: 0.7490 (mptt) REVERT: A 708 ARG cc_start: 0.2338 (OUTLIER) cc_final: 0.0941 (ptp90) REVERT: A 765 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7432 (mm) REVERT: A 772 ILE cc_start: 0.5650 (OUTLIER) cc_final: 0.5313 (mm) REVERT: A 849 ILE cc_start: 0.5152 (OUTLIER) cc_final: 0.4542 (mm) REVERT: A 869 PHE cc_start: 0.0290 (OUTLIER) cc_final: -0.0147 (m-10) REVERT: B 60 LYS cc_start: 0.6532 (mptt) cc_final: 0.6273 (mptt) REVERT: B 158 LYS cc_start: 0.8922 (tppt) cc_final: 0.8140 (tmtt) REVERT: B 428 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7951 (mtpm) REVERT: B 551 ASN cc_start: 0.7295 (m-40) cc_final: 0.6674 (t0) REVERT: B 597 SER cc_start: 0.8812 (t) cc_final: 0.8575 (t) REVERT: B 736 HIS cc_start: 0.6275 (OUTLIER) cc_final: 0.5324 (t-90) REVERT: B 825 LEU cc_start: 0.0640 (OUTLIER) cc_final: -0.0149 (tp) REVERT: B 833 TYR cc_start: 0.6356 (m-80) cc_final: 0.5867 (m-80) REVERT: B 840 LEU cc_start: 0.4246 (OUTLIER) cc_final: 0.3620 (tp) REVERT: B 894 MET cc_start: 0.0772 (mmm) cc_final: -0.0237 (tpt) REVERT: B 932 MET cc_start: 0.3747 (OUTLIER) cc_final: 0.3436 (ptp) REVERT: B 942 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.3925 (mp) REVERT: C 33 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7681 (mtm110) REVERT: C 136 ARG cc_start: 0.8211 (ttm170) cc_final: 0.7814 (ttm-80) REVERT: C 263 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: C 451 MET cc_start: 0.8737 (mtp) cc_final: 0.8128 (mmt) REVERT: C 615 LYS cc_start: 0.5032 (mttm) cc_final: 0.4729 (mmtp) REVERT: C 685 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5686 (pm20) REVERT: C 698 PHE cc_start: 0.5151 (OUTLIER) cc_final: 0.4679 (t80) REVERT: C 741 GLN cc_start: 0.6024 (mm110) cc_final: 0.5116 (tt0) REVERT: C 809 ILE cc_start: 0.5789 (OUTLIER) cc_final: 0.4975 (mm) REVERT: C 833 TYR cc_start: 0.6548 (m-10) cc_final: 0.5700 (m-80) REVERT: C 871 HIS cc_start: 0.4451 (t-90) cc_final: 0.2495 (m90) REVERT: C 894 MET cc_start: 0.6166 (tpp) cc_final: 0.5720 (tpp) REVERT: C 896 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4738 (tt) REVERT: C 910 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6294 (tp) REVERT: C 932 MET cc_start: -0.0300 (OUTLIER) cc_final: -0.0733 (ppp) REVERT: C 972 MET cc_start: 0.7382 (tpp) cc_final: 0.6977 (tpp) REVERT: D 53 GLN cc_start: 0.7400 (tp40) cc_final: 0.6979 (tp-100) REVERT: D 60 LYS cc_start: 0.8116 (tptt) cc_final: 0.7733 (mttp) REVERT: D 76 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7928 (p0) REVERT: D 103 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.7956 (p) REVERT: D 491 MET cc_start: 0.7486 (tmm) cc_final: 0.7187 (ttp) REVERT: D 518 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: D 530 SER cc_start: 0.8512 (OUTLIER) cc_final: 0.7862 (p) REVERT: D 566 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.6840 (tptp) REVERT: D 774 TRP cc_start: 0.7148 (t60) cc_final: 0.6507 (t60) REVERT: D 975 PHE cc_start: 0.0442 (OUTLIER) cc_final: 0.0152 (m-80) outliers start: 195 outliers final: 138 residues processed: 397 average time/residue: 0.1972 time to fit residues: 131.6188 Evaluate side-chains 387 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 219 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 238 ASN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 794 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 853 PHE Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 496 CYS Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 683 SER Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 695 SER Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 820 SER Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 100 ILE Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 325 GLU Chi-restraints excluded: chain D residue 398 THR Chi-restraints excluded: chain D residue 412 ASP Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 490 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 518 GLU Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 606 VAL Chi-restraints excluded: chain D residue 608 MET Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 639 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 717 ILE Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 852 SER Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 328 optimal weight: 0.2980 chunk 355 optimal weight: 0.9990 chunk 198 optimal weight: 20.0000 chunk 408 optimal weight: 20.0000 chunk 244 optimal weight: 1.9990 chunk 321 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 250 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 190 optimal weight: 20.0000 chunk 180 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 GLN ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 876 ASN ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.144691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.093602 restraints weight = 76819.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.096027 restraints weight = 44389.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.096214 restraints weight = 32251.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096796 restraints weight = 24819.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.097304 restraints weight = 22646.591| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34053 Z= 0.112 Angle : 0.609 12.475 46077 Z= 0.299 Chirality : 0.043 0.198 5286 Planarity : 0.004 0.057 5831 Dihedral : 7.189 171.950 4561 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.09 % Favored : 91.65 % Rotamer: Outliers : 3.98 % Allowed : 29.39 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 4178 helix: 1.19 (0.15), residues: 1365 sheet: -2.14 (0.26), residues: 395 loop : -2.05 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 579 TYR 0.017 0.001 TYR B 515 PHE 0.019 0.001 PHE A 265 TRP 0.028 0.001 TRP B 774 HIS 0.008 0.001 HIS B 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (34043) covalent geometry : angle 0.60840 / 0.30 (46057) SS BOND : bond 0.00315 / 0.24 ( 10) SS BOND : angle 1.12408 / 0.61 ( 20) hydrogen bonds : bond 0.03072 / 2.13 ( 1025) hydrogen bonds : angle 4.81072 / 3.43 ( 2979) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 229 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.7687 (tp30) cc_final: 0.6831 (tp30) REVERT: A 136 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: A 232 SER cc_start: 0.8412 (OUTLIER) cc_final: 0.8131 (p) REVERT: A 556 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6118 (tptm) REVERT: A 573 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7375 (mt-10) REVERT: A 631 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 673 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6195 (tt) REVERT: A 703 LYS cc_start: 0.7703 (mptt) cc_final: 0.7446 (mptt) REVERT: A 708 ARG cc_start: 0.2381 (OUTLIER) cc_final: 0.0601 (mtm-85) REVERT: A 765 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7395 (mm) REVERT: A 772 ILE cc_start: 0.5548 (OUTLIER) cc_final: 0.5215 (mm) REVERT: A 849 ILE cc_start: 0.5166 (OUTLIER) cc_final: 0.4550 (mm) REVERT: A 869 PHE cc_start: 0.0256 (OUTLIER) cc_final: -0.0166 (m-10) REVERT: B 60 LYS cc_start: 0.6230 (mptt) cc_final: 0.5962 (mptt) REVERT: B 451 MET cc_start: 0.8207 (mmp) cc_final: 0.7891 (mmp) REVERT: B 736 HIS cc_start: 0.6212 (OUTLIER) cc_final: 0.5240 (t-90) REVERT: B 825 LEU cc_start: 0.0875 (OUTLIER) cc_final: 0.0041 (tp) REVERT: B 833 TYR cc_start: 0.6405 (m-80) cc_final: 0.5908 (m-80) REVERT: B 840 LEU cc_start: 0.4217 (OUTLIER) cc_final: 0.3594 (tp) REVERT: B 894 MET cc_start: 0.0681 (mmm) cc_final: -0.0148 (tpp) REVERT: B 932 MET cc_start: 0.3718 (OUTLIER) cc_final: 0.3463 (ptp) REVERT: B 942 LEU cc_start: 0.4943 (OUTLIER) cc_final: 0.4005 (mt) REVERT: C 33 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7472 (mtm110) REVERT: C 136 ARG cc_start: 0.8215 (ttm170) cc_final: 0.7856 (ttm-80) REVERT: C 163 MET cc_start: 0.8548 (tmm) cc_final: 0.8107 (ttt) REVERT: C 263 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: C 615 LYS cc_start: 0.5064 (mttm) cc_final: 0.4767 (mmtp) REVERT: C 685 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: C 698 PHE cc_start: 0.5046 (OUTLIER) cc_final: 0.4630 (t80) REVERT: C 741 GLN cc_start: 0.6044 (mm110) cc_final: 0.5138 (tt0) REVERT: C 764 HIS cc_start: 0.6863 (t-90) cc_final: 0.6599 (t-170) REVERT: C 809 ILE cc_start: 0.5858 (OUTLIER) cc_final: 0.5056 (mm) REVERT: C 833 TYR cc_start: 0.6478 (m-10) cc_final: 0.5626 (m-80) REVERT: C 871 HIS cc_start: 0.4425 (t-90) cc_final: 0.2375 (m90) REVERT: C 894 MET cc_start: 0.6166 (tpp) cc_final: 0.5711 (tpp) REVERT: C 896 LEU cc_start: 0.4887 (OUTLIER) cc_final: 0.4652 (tt) REVERT: C 910 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6348 (tp) REVERT: C 932 MET cc_start: -0.0266 (OUTLIER) cc_final: -0.1013 (ppp) REVERT: C 972 MET cc_start: 0.7449 (tpp) cc_final: 0.7074 (tpp) REVERT: D 53 GLN cc_start: 0.7279 (tp40) cc_final: 0.6840 (tp40) REVERT: D 60 LYS cc_start: 0.8048 (tptt) cc_final: 0.7704 (mttt) REVERT: D 76 ASN cc_start: 0.8203 (OUTLIER) cc_final: 0.7882 (p0) REVERT: D 103 THR cc_start: 0.8123 (OUTLIER) cc_final: 0.7821 (p) REVERT: D 530 SER cc_start: 0.8466 (OUTLIER) cc_final: 0.7826 (p) REVERT: D 566 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.6826 (tptp) REVERT: D 639 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6476 (pm20) REVERT: D 774 TRP cc_start: 0.7234 (t60) cc_final: 0.6576 (t60) REVERT: D 975 PHE cc_start: 0.0524 (OUTLIER) cc_final: 0.0202 (m-80) outliers start: 150 outliers final: 102 residues processed: 360 average time/residue: 0.2015 time to fit residues: 122.2267 Evaluate side-chains 353 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 221 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 136 ARG Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 608 MET Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 50 GLU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 794 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 109 ASP Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 826 ASN Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 639 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 772 ILE Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 81 optimal weight: 6.9990 chunk 113 optimal weight: 0.0470 chunk 293 optimal weight: 9.9990 chunk 313 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 340 optimal weight: 0.6980 chunk 169 optimal weight: 9.9990 chunk 137 optimal weight: 0.0050 chunk 329 optimal weight: 1.9990 overall best weight: 1.1496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.144098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.093059 restraints weight = 76611.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095622 restraints weight = 43892.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.095702 restraints weight = 30579.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.096394 restraints weight = 24191.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.096753 restraints weight = 22872.565| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34053 Z= 0.129 Angle : 0.621 13.707 46077 Z= 0.302 Chirality : 0.043 0.210 5286 Planarity : 0.004 0.056 5831 Dihedral : 7.123 170.760 4557 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.76 % Favored : 90.98 % Rotamer: Outliers : 3.93 % Allowed : 29.36 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4178 helix: 1.22 (0.15), residues: 1365 sheet: -2.19 (0.26), residues: 412 loop : -2.02 (0.12), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 579 TYR 0.017 0.001 TYR B 515 PHE 0.016 0.001 PHE A 265 TRP 0.030 0.001 TRP B 774 HIS 0.011 0.001 HIS B 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (34043) covalent geometry : angle 0.62033 / 0.30 (46057) SS BOND : bond 0.00147 / 0.08 ( 10) SS BOND : angle 0.99215 / 0.58 ( 20) hydrogen bonds : bond 0.03148 / 2.19 ( 1025) hydrogen bonds : angle 4.77707 / 3.41 ( 2979) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 229 time to evaluate : 1.381 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 135 GLU cc_start: 0.7677 (tp30) cc_final: 0.6763 (tp30) REVERT: A 232 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8139 (p) REVERT: A 556 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6134 (tptm) REVERT: A 573 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: A 631 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7303 (pp) REVERT: A 673 LEU cc_start: 0.6578 (OUTLIER) cc_final: 0.6202 (tt) REVERT: A 703 LYS cc_start: 0.7718 (mptt) cc_final: 0.7450 (mptt) REVERT: A 708 ARG cc_start: 0.2339 (OUTLIER) cc_final: 0.0637 (mtm-85) REVERT: A 710 PHE cc_start: 0.6490 (t80) cc_final: 0.6158 (t80) REVERT: A 765 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7327 (mm) REVERT: A 772 ILE cc_start: 0.5634 (OUTLIER) cc_final: 0.5304 (mm) REVERT: A 849 ILE cc_start: 0.5166 (OUTLIER) cc_final: 0.4577 (mm) REVERT: A 869 PHE cc_start: 0.0288 (OUTLIER) cc_final: -0.0120 (m-10) REVERT: B 209 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7531 (ttp) REVERT: B 428 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7893 (mtpm) REVERT: B 551 ASN cc_start: 0.7337 (m-40) cc_final: 0.6667 (t0) REVERT: B 597 SER cc_start: 0.8801 (t) cc_final: 0.8439 (p) REVERT: B 736 HIS cc_start: 0.6009 (OUTLIER) cc_final: 0.4909 (t-90) REVERT: B 738 SER cc_start: 0.8649 (t) cc_final: 0.8167 (p) REVERT: B 825 LEU cc_start: 0.0778 (OUTLIER) cc_final: -0.0043 (tp) REVERT: B 833 TYR cc_start: 0.6399 (m-80) cc_final: 0.5916 (m-80) REVERT: B 840 LEU cc_start: 0.3950 (OUTLIER) cc_final: 0.3417 (tp) REVERT: B 894 MET cc_start: 0.0794 (mmm) cc_final: -0.0141 (tpp) REVERT: B 932 MET cc_start: 0.3768 (OUTLIER) cc_final: 0.3546 (ptp) REVERT: B 942 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.3961 (mt) REVERT: C 33 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7595 (mtm110) REVERT: C 136 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7911 (ttm170) REVERT: C 263 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: C 615 LYS cc_start: 0.5127 (mttm) cc_final: 0.4781 (mmtp) REVERT: C 685 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5629 (pm20) REVERT: C 698 PHE cc_start: 0.5219 (OUTLIER) cc_final: 0.4802 (t80) REVERT: C 741 GLN cc_start: 0.6002 (mm110) cc_final: 0.5145 (tt0) REVERT: C 809 ILE cc_start: 0.5796 (OUTLIER) cc_final: 0.4995 (mm) REVERT: C 833 TYR cc_start: 0.6460 (m-10) cc_final: 0.5590 (m-80) REVERT: C 871 HIS cc_start: 0.4494 (t-90) cc_final: 0.2388 (m90) REVERT: C 894 MET cc_start: 0.6239 (tpp) cc_final: 0.5798 (tpp) REVERT: C 896 LEU cc_start: 0.4909 (OUTLIER) cc_final: 0.4695 (tt) REVERT: C 910 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6373 (tp) REVERT: C 932 MET cc_start: -0.0374 (OUTLIER) cc_final: -0.1072 (ppp) REVERT: C 972 MET cc_start: 0.7417 (tpp) cc_final: 0.7075 (tpp) REVERT: D 53 GLN cc_start: 0.7317 (tp40) cc_final: 0.6937 (tp-100) REVERT: D 60 LYS cc_start: 0.8018 (tptt) cc_final: 0.7638 (mtmt) REVERT: D 76 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7929 (p0) REVERT: D 103 THR cc_start: 0.8132 (OUTLIER) cc_final: 0.7821 (p) REVERT: D 530 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.7836 (p) REVERT: D 566 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7025 (tptp) REVERT: D 599 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: D 774 TRP cc_start: 0.7283 (t60) cc_final: 0.6639 (t60) REVERT: D 975 PHE cc_start: 0.0457 (OUTLIER) cc_final: 0.0156 (m-80) outliers start: 148 outliers final: 103 residues processed: 359 average time/residue: 0.2042 time to fit residues: 123.1052 Evaluate side-chains 354 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 220 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 949 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 794 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 932 MET Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 33 ARG Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 792 SER Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 829 ASN Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 639 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 394 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 173 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 169 optimal weight: 0.0060 chunk 263 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.144631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.093572 restraints weight = 76999.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.096376 restraints weight = 43964.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.096459 restraints weight = 30032.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.097375 restraints weight = 24128.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.097643 restraints weight = 22353.905| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34053 Z= 0.118 Angle : 0.616 14.279 46077 Z= 0.301 Chirality : 0.043 0.207 5286 Planarity : 0.004 0.059 5831 Dihedral : 7.062 168.574 4557 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 3.69 % Allowed : 29.66 % Favored : 66.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.13), residues: 4178 helix: 1.26 (0.15), residues: 1365 sheet: -2.11 (0.26), residues: 413 loop : -2.01 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 579 TYR 0.020 0.001 TYR B 515 PHE 0.017 0.001 PHE A 265 TRP 0.031 0.001 TRP B 774 HIS 0.011 0.001 HIS B 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (34043) covalent geometry : angle 0.61620 / 0.30 (46057) SS BOND : bond 0.00128 / 0.07 ( 10) SS BOND : angle 0.75224 / 0.47 ( 20) hydrogen bonds : bond 0.03011 / 2.09 ( 1025) hydrogen bonds : angle 4.73128 / 3.38 ( 2979) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 230 time to evaluate : 1.361 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 135 GLU cc_start: 0.7671 (tp30) cc_final: 0.6736 (tp30) REVERT: A 232 SER cc_start: 0.8400 (OUTLIER) cc_final: 0.8089 (p) REVERT: A 556 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6113 (tptm) REVERT: A 573 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: A 631 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7309 (pp) REVERT: A 673 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6169 (tt) REVERT: A 703 LYS cc_start: 0.7772 (mptt) cc_final: 0.7500 (mptt) REVERT: A 708 ARG cc_start: 0.2197 (OUTLIER) cc_final: 0.1032 (ptp90) REVERT: A 710 PHE cc_start: 0.6501 (t80) cc_final: 0.6186 (t80) REVERT: A 765 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7357 (mm) REVERT: A 772 ILE cc_start: 0.5589 (OUTLIER) cc_final: 0.5252 (mm) REVERT: A 849 ILE cc_start: 0.5215 (OUTLIER) cc_final: 0.4650 (mm) REVERT: A 869 PHE cc_start: 0.0516 (OUTLIER) cc_final: 0.0059 (m-10) REVERT: B 551 ASN cc_start: 0.7373 (m-40) cc_final: 0.6659 (t0) REVERT: B 597 SER cc_start: 0.8804 (t) cc_final: 0.8398 (p) REVERT: B 736 HIS cc_start: 0.6056 (OUTLIER) cc_final: 0.5116 (t-90) REVERT: B 738 SER cc_start: 0.8665 (t) cc_final: 0.8192 (p) REVERT: B 825 LEU cc_start: 0.0876 (OUTLIER) cc_final: 0.0017 (tp) REVERT: B 833 TYR cc_start: 0.6368 (m-80) cc_final: 0.5926 (m-80) REVERT: B 840 LEU cc_start: 0.3795 (OUTLIER) cc_final: 0.3264 (tp) REVERT: B 894 MET cc_start: 0.0812 (mmm) cc_final: -0.0095 (tpp) REVERT: B 942 LEU cc_start: 0.4930 (OUTLIER) cc_final: 0.3970 (mt) REVERT: C 136 ARG cc_start: 0.8245 (ttm170) cc_final: 0.7934 (ttm-80) REVERT: C 163 MET cc_start: 0.8555 (tmm) cc_final: 0.8099 (ttt) REVERT: C 263 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: C 615 LYS cc_start: 0.5133 (mttm) cc_final: 0.4770 (mmtp) REVERT: C 677 MET cc_start: 0.6338 (mmt) cc_final: 0.5941 (mmm) REVERT: C 685 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5554 (pm20) REVERT: C 698 PHE cc_start: 0.5173 (OUTLIER) cc_final: 0.4942 (t80) REVERT: C 741 GLN cc_start: 0.6032 (mm110) cc_final: 0.5185 (tt0) REVERT: C 764 HIS cc_start: 0.6928 (t-90) cc_final: 0.6648 (t-170) REVERT: C 809 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5108 (mm) REVERT: C 833 TYR cc_start: 0.6530 (m-10) cc_final: 0.5670 (m-80) REVERT: C 871 HIS cc_start: 0.4606 (t-90) cc_final: 0.2442 (m90) REVERT: C 894 MET cc_start: 0.6225 (tpp) cc_final: 0.5783 (tpp) REVERT: C 896 LEU cc_start: 0.4825 (OUTLIER) cc_final: 0.4618 (tt) REVERT: C 910 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6425 (tp) REVERT: C 932 MET cc_start: -0.0343 (OUTLIER) cc_final: -0.1081 (ppp) REVERT: C 972 MET cc_start: 0.7410 (tpp) cc_final: 0.7095 (tpp) REVERT: D 53 GLN cc_start: 0.7310 (tp40) cc_final: 0.6858 (tp40) REVERT: D 60 LYS cc_start: 0.7951 (tptt) cc_final: 0.7660 (mttt) REVERT: D 76 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7895 (p0) REVERT: D 103 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7783 (p) REVERT: D 530 SER cc_start: 0.8457 (OUTLIER) cc_final: 0.7816 (p) REVERT: D 566 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.6979 (tptp) REVERT: D 599 PHE cc_start: 0.6761 (OUTLIER) cc_final: 0.6499 (m-80) REVERT: D 975 PHE cc_start: 0.0483 (OUTLIER) cc_final: 0.0181 (m-80) outliers start: 139 outliers final: 103 residues processed: 354 average time/residue: 0.2032 time to fit residues: 122.2188 Evaluate side-chains 353 residues out of total 3774 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 223 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 410 CYS Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 526 ILE Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 573 GLU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 658 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain A residue 698 PHE Chi-restraints excluded: chain A residue 708 ARG Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 772 ILE Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 808 LYS Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 815 CYS Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 869 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 497 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 592 LYS Chi-restraints excluded: chain B residue 599 PHE Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 622 CYS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 691 ILE Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 736 HIS Chi-restraints excluded: chain B residue 764 HIS Chi-restraints excluded: chain B residue 794 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 832 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 898 HIS Chi-restraints excluded: chain B residue 938 VAL Chi-restraints excluded: chain B residue 942 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 263 GLU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 679 TYR Chi-restraints excluded: chain C residue 685 GLU Chi-restraints excluded: chain C residue 687 ILE Chi-restraints excluded: chain C residue 698 PHE Chi-restraints excluded: chain C residue 720 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 809 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 896 LEU Chi-restraints excluded: chain C residue 904 LEU Chi-restraints excluded: chain C residue 910 LEU Chi-restraints excluded: chain C residue 932 MET Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain D residue 41 ILE Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 50 GLU Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 298 ASP Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 497 THR Chi-restraints excluded: chain D residue 530 SER Chi-restraints excluded: chain D residue 563 HIS Chi-restraints excluded: chain D residue 566 LYS Chi-restraints excluded: chain D residue 599 PHE Chi-restraints excluded: chain D residue 623 LEU Chi-restraints excluded: chain D residue 639 GLU Chi-restraints excluded: chain D residue 643 LEU Chi-restraints excluded: chain D residue 725 THR Chi-restraints excluded: chain D residue 779 CYS Chi-restraints excluded: chain D residue 814 ASP Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 827 THR Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 888 PHE Chi-restraints excluded: chain D residue 933 PHE Chi-restraints excluded: chain D residue 938 VAL Chi-restraints excluded: chain D residue 975 PHE Chi-restraints excluded: chain D residue 983 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 416 random chunks: chunk 307 optimal weight: 9.9990 chunk 257 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 chunk 302 optimal weight: 1.9990 chunk 391 optimal weight: 10.0000 chunk 128 optimal weight: 0.5980 chunk 132 optimal weight: 7.9990 chunk 374 optimal weight: 8.9990 chunk 122 optimal weight: 0.0980 chunk 9 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 766 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 899 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 811 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.143389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092209 restraints weight = 76772.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.094812 restraints weight = 43847.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.094826 restraints weight = 31126.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.095625 restraints weight = 24901.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.096043 restraints weight = 22523.038| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34053 Z= 0.161 Angle : 0.638 14.246 46077 Z= 0.313 Chirality : 0.044 0.242 5286 Planarity : 0.004 0.057 5831 Dihedral : 7.168 170.801 4557 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.81 % Favored : 90.98 % Rotamer: Outliers : 3.79 % Allowed : 29.58 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.13), residues: 4178 helix: 1.16 (0.15), residues: 1365 sheet: -2.12 (0.25), residues: 439 loop : -2.03 (0.12), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 579 TYR 0.019 0.001 TYR B 515 PHE 0.015 0.001 PHE A 265 TRP 0.032 0.001 TRP B 774 HIS 0.011 0.001 HIS B 899 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (34043) covalent geometry : angle 0.63825 / 0.31 (46057) SS BOND : bond 0.00128 / 0.07 ( 10) SS BOND : angle 0.77250 / 0.49 ( 20) hydrogen bonds : bond 0.03376 / 2.35 ( 1025) hydrogen bonds : angle 4.80285 / 3.42 ( 2979) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7403.87 seconds wall clock time: 129 minutes 36.78 seconds (7776.78 seconds total)