Starting phenix.real_space_refine on Fri Mar 6 19:11:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hki_34852/03_2026/8hki_34852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hki_34852/03_2026/8hki_34852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hki_34852/03_2026/8hki_34852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hki_34852/03_2026/8hki_34852.map" model { file = "/net/cci-nas-00/data/ceres_data/8hki_34852/03_2026/8hki_34852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hki_34852/03_2026/8hki_34852.cif" } resolution = 3.1 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= 0.014 sd= 0.124 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 12 5.49 5 S 189 5.16 5 C 21156 2.51 5 N 5930 2.21 5 O 6639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33926 Number of models: 1 Model: "" Number of chains: 22 Chain: "a" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2182 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 8, 'TRANS': 282} Chain breaks: 2 Chain: "A" Number of atoms: 1918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1918 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Chain: "b" Number of atoms: 2407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2407 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 6, 'TRANS': 320} Chain breaks: 3 Chain: "B" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1842 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 6, 'TRANS': 243} Chain breaks: 1 Chain: "D" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1870 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain breaks: 1 Chain: "d" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2086 Classifications: {'peptide': 278} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 1 Chain: "E" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1916 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 2 Chain: "e" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2433 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 8, 'TRANS': 312} Chain breaks: 2 Chain: "g" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1822 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 7, 'TRANS': 231} Chain breaks: 1 Chain: "G" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1946 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "h" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2585 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 9, 'TRANS': 329} Chain breaks: 2 Chain: "H" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1929 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain breaks: 2 Chain: "Q" Number of atoms: 1998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 1998 Classifications: {'peptide': 262} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 252} Chain breaks: 1 Chain: "q" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2574 Classifications: {'peptide': 338} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 328} Chain breaks: 2 Chain: "Z" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1887 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Chain: "z" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2369 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "z" 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: 7.30, per 1000 atoms: 0.22 Number of scatterers: 33926 At special positions: 0 Unit cell: (187.156, 108.076, 181.884, 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 189 16.00 P 12 15.00 O 6639 8.00 N 5930 7.00 C 21156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8324 Finding SS restraints... Secondary structure from input PDB file: 201 helices and 43 sheets defined 67.6% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'a' and resid 14 through 31 removed outlier: 4.307A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 removed outlier: 3.506A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.561A pdb=" N GLU a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 134 Processing helix chain 'a' and resid 148 through 157 Processing helix chain 'a' and resid 159 through 164 removed outlier: 3.603A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN a 164 " --> pdb=" O ILE a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 413 through 431 removed outlier: 3.811A pdb=" N ILE a 421 " --> pdb=" O ALA a 417 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET a 430 " --> pdb=" O TYR a 426 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY a 431 " --> pdb=" O ALA a 427 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 446 removed outlier: 3.554A pdb=" N LEU a 445 " --> pdb=" O PHE a 441 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 removed outlier: 3.517A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN a 477 " --> pdb=" O GLU a 473 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'A' and resid 14 through 32 removed outlier: 3.937A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 removed outlier: 3.616A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 133 Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.679A pdb=" N ILE A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 424 " --> pdb=" O SER A 420 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET A 430 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 446 removed outlier: 3.564A pdb=" N LEU A 445 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.804A pdb=" N ASN A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.710A pdb=" N LYS A 510 " --> pdb=" O PRO A 506 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 514 " --> pdb=" O LYS A 510 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 40 removed outlier: 3.755A pdb=" N LEU b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE b 29 " --> pdb=" O ARG b 25 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE b 35 " --> pdb=" O GLY b 31 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 74 removed outlier: 3.572A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) Processing helix chain 'b' and resid 78 through 95 removed outlier: 3.766A pdb=" N GLN b 91 " --> pdb=" O MET b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 119 removed outlier: 3.504A pdb=" N THR b 103 " --> pdb=" O THR b 99 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER b 115 " --> pdb=" O ARG b 111 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 145 removed outlier: 3.580A pdb=" N GLY b 129 " --> pdb=" O THR b 125 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU b 141 " --> pdb=" O ALA b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 168 Processing helix chain 'b' and resid 170 through 174 removed outlier: 4.514A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 379 through 403 removed outlier: 3.625A pdb=" N LEU b 383 " --> pdb=" O THR b 379 " (cutoff:3.500A) Processing helix chain 'b' and resid 411 through 425 Processing helix chain 'b' and resid 429 through 455 removed outlier: 3.858A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER b 438 " --> pdb=" O VAL b 434 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU b 446 " --> pdb=" O ALA b 442 " (cutoff:3.500A) Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 457 through 471 removed outlier: 3.667A pdb=" N GLU b 471 " --> pdb=" O ALA b 467 " (cutoff:3.500A) Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 removed outlier: 3.511A pdb=" N ILE b 514 " --> pdb=" O ALA b 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 39 removed outlier: 3.647A pdb=" N ILE B 35 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 66 through 74 removed outlier: 3.790A pdb=" N ASN B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 94 removed outlier: 3.571A pdb=" N LYS B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.711A pdb=" N SER B 115 " --> pdb=" O ARG B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 429 through 455 removed outlier: 3.960A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 457 through 470 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 496 through 516 Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.708A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.529A pdb=" N GLN D 80 " --> pdb=" O THR D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.768A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 Processing helix chain 'D' and resid 426 through 443 removed outlier: 3.725A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG D 441 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.692A pdb=" N MET D 458 " --> pdb=" O PHE D 454 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'd' and resid 30 through 50 removed outlier: 3.936A pdb=" N ARG d 34 " --> pdb=" O PRO d 30 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL d 44 " --> pdb=" O ALA d 40 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR d 50 " --> pdb=" O ASP d 46 " (cutoff:3.500A) Processing helix chain 'd' and resid 73 through 80 Processing helix chain 'd' and resid 85 through 102 removed outlier: 3.691A pdb=" N LEU d 91 " --> pdb=" O ALA d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.958A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN d 125 " --> pdb=" O THR d 121 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS d 126 " --> pdb=" O LYS d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 129 through 151 removed outlier: 3.605A pdb=" N GLU d 146 " --> pdb=" O GLU d 142 " (cutoff:3.500A) Processing helix chain 'd' and resid 159 through 174 removed outlier: 3.835A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 426 through 443 removed outlier: 3.564A pdb=" N ARG d 441 " --> pdb=" O THR d 437 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 459 removed outlier: 3.682A pdb=" N MET d 458 " --> pdb=" O PHE d 454 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU d 459 " --> pdb=" O ALA d 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 469 Processing helix chain 'd' and resid 472 through 487 removed outlier: 3.739A pdb=" N VAL d 477 " --> pdb=" O PRO d 473 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN d 482 " --> pdb=" O THR d 478 " (cutoff:3.500A) Processing helix chain 'd' and resid 503 through 507 Processing helix chain 'd' and resid 512 through 531 Processing helix chain 'E' and resid 28 through 48 removed outlier: 3.520A pdb=" N MET E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR E 48 " --> pdb=" O ASN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 79 Processing helix chain 'E' and resid 83 through 100 removed outlier: 3.524A pdb=" N MET E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 125 removed outlier: 3.635A pdb=" N VAL E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 removed outlier: 3.826A pdb=" N ASP E 147 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 436 removed outlier: 3.938A pdb=" N ASP E 436 " --> pdb=" O SER E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 454 removed outlier: 4.196A pdb=" N ALA E 445 " --> pdb=" O LEU E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 464 Processing helix chain 'E' and resid 467 through 479 Processing helix chain 'E' and resid 498 through 503 removed outlier: 3.670A pdb=" N GLN E 502 " --> pdb=" O ASP E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 527 Processing helix chain 'e' and resid 28 through 47 removed outlier: 3.554A pdb=" N LEU e 32 " --> pdb=" O GLY e 28 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL e 42 " --> pdb=" O ALA e 38 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 50 No H-bonds generated for 'chain 'e' and resid 48 through 50' Processing helix chain 'e' and resid 71 through 79 Processing helix chain 'e' and resid 83 through 97 removed outlier: 4.132A pdb=" N SER e 93 " --> pdb=" O MET e 89 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS e 94 " --> pdb=" O VAL e 90 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER e 95 " --> pdb=" O GLU e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 124 removed outlier: 3.861A pdb=" N GLN e 120 " --> pdb=" O GLU e 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU e 121 " --> pdb=" O GLU e 117 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG e 124 " --> pdb=" O GLN e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 127 through 150 removed outlier: 3.568A pdb=" N ASP e 147 " --> pdb=" O ILE e 143 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS e 148 " --> pdb=" O GLU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 160 through 172 removed outlier: 3.522A pdb=" N ILE e 164 " --> pdb=" O THR e 160 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA e 167 " --> pdb=" O LEU e 163 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR e 169 " --> pdb=" O GLN e 165 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY e 172 " --> pdb=" O LYS e 168 " (cutoff:3.500A) Processing helix chain 'e' and resid 173 through 180 removed outlier: 6.675A pdb=" N VAL e 176 " --> pdb=" O SER e 173 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER e 178 " --> pdb=" O VAL e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 216 through 220 Processing helix chain 'e' and resid 389 through 413 removed outlier: 3.547A pdb=" N LEU e 400 " --> pdb=" O ALA e 396 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA e 403 " --> pdb=" O SER e 399 " (cutoff:3.500A) Processing helix chain 'e' and resid 421 through 436 removed outlier: 3.559A pdb=" N LEU e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP e 436 " --> pdb=" O SER e 432 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 454 removed outlier: 4.321A pdb=" N ALA e 445 " --> pdb=" O LEU e 441 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 465 Processing helix chain 'e' and resid 467 through 481 Processing helix chain 'e' and resid 498 through 503 removed outlier: 3.836A pdb=" N GLN e 502 " --> pdb=" O ASP e 498 " (cutoff:3.500A) Processing helix chain 'e' and resid 508 through 527 Processing helix chain 'g' and resid 19 through 37 removed outlier: 4.253A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 70 Processing helix chain 'g' and resid 74 through 91 removed outlier: 3.510A pdb=" N LYS g 78 " --> pdb=" O HIS g 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 94 through 107 removed outlier: 3.659A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 139 removed outlier: 3.578A pdb=" N ASP g 131 " --> pdb=" O ARG g 127 " (cutoff:3.500A) Processing helix chain 'g' and resid 414 through 426 removed outlier: 3.546A pdb=" N ALA g 421 " --> pdb=" O ALA g 417 " (cutoff:3.500A) Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 433 through 445 removed outlier: 3.821A pdb=" N ALA g 441 " --> pdb=" O TYR g 437 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) Processing helix chain 'g' and resid 445 through 456 removed outlier: 3.506A pdb=" N CYS g 455 " --> pdb=" O LEU g 451 " (cutoff:3.500A) Processing helix chain 'g' and resid 458 through 473 removed outlier: 3.514A pdb=" N LEU g 462 " --> pdb=" O SER g 458 " (cutoff:3.500A) Processing helix chain 'g' and resid 498 through 519 removed outlier: 3.885A pdb=" N LYS g 502 " --> pdb=" O PRO g 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 37 removed outlier: 4.064A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 74 through 91 removed outlier: 3.638A pdb=" N SER G 84 " --> pdb=" O MET G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 107 removed outlier: 3.626A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.760A pdb=" N LYS G 139 " --> pdb=" O SER G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 426 Processing helix chain 'G' and resid 427 through 429 No H-bonds generated for 'chain 'G' and resid 427 through 429' Processing helix chain 'G' and resid 433 through 444 removed outlier: 3.778A pdb=" N ALA G 441 " --> pdb=" O TYR G 437 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 473 Processing helix chain 'G' and resid 499 through 519 Processing helix chain 'h' and resid 18 through 35 Processing helix chain 'h' and resid 61 through 70 removed outlier: 3.875A pdb=" N ASP h 70 " --> pdb=" O LEU h 66 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 90 removed outlier: 3.573A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 108 Processing helix chain 'h' and resid 108 through 114 Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.594A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA h 124 " --> pdb=" O ILE h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 145 through 149 Processing helix chain 'h' and resid 150 through 164 removed outlier: 3.538A pdb=" N LEU h 154 " --> pdb=" O GLU h 150 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 184 Processing helix chain 'h' and resid 378 through 402 removed outlier: 3.678A pdb=" N MET h 382 " --> pdb=" O ALA h 378 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG h 387 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA h 392 " --> pdb=" O SER h 388 " (cutoff:3.500A) Processing helix chain 'h' and resid 410 through 426 removed outlier: 3.993A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 442 removed outlier: 3.763A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU h 442 " --> pdb=" O TYR h 438 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 453 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.545A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE H 32 " --> pdb=" O ALA H 28 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 70 removed outlier: 3.576A pdb=" N LEU H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 90 removed outlier: 3.631A pdb=" N THR H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 108 Processing helix chain 'H' and resid 108 through 114 Processing helix chain 'H' and resid 117 through 139 removed outlier: 3.623A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN H 130 " --> pdb=" O ARG H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 426 removed outlier: 3.550A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 442 removed outlier: 3.784A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 442 " --> pdb=" O TYR H 438 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 453 removed outlier: 3.538A pdb=" N LEU H 449 " --> pdb=" O ILE H 445 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS H 450 " --> pdb=" O PRO H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 456 through 471 removed outlier: 3.501A pdb=" N ALA H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 495 through 515 Processing helix chain 'Q' and resid 27 through 45 removed outlier: 3.517A pdb=" N ASN Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS Q 36 " --> pdb=" O ASN Q 32 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 95 removed outlier: 4.116A pdb=" N ILE Q 86 " --> pdb=" O ALA Q 82 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN Q 95 " --> pdb=" O HIS Q 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 122 removed outlier: 4.038A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU Q 118 " --> pdb=" O LEU Q 114 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE Q 121 " --> pdb=" O GLU Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 143 removed outlier: 3.528A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 430 Processing helix chain 'Q' and resid 433 through 446 removed outlier: 4.305A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 456 Processing helix chain 'Q' and resid 459 through 473 removed outlier: 3.506A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 500 through 520 Processing helix chain 'q' and resid 27 through 45 removed outlier: 3.672A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR q 42 " --> pdb=" O GLU q 38 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 95 removed outlier: 4.128A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN q 95 " --> pdb=" O HIS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 122 removed outlier: 3.738A pdb=" N GLU q 117 " --> pdb=" O GLU q 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 156 through 169 removed outlier: 3.554A pdb=" N ARG q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 175 through 187 removed outlier: 3.619A pdb=" N ALA q 186 " --> pdb=" O LEU q 182 " (cutoff:3.500A) Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 381 through 403 removed outlier: 3.579A pdb=" N ARG q 390 " --> pdb=" O ASP q 386 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE q 399 " --> pdb=" O GLY q 395 " (cutoff:3.500A) Processing helix chain 'q' and resid 413 through 430 Processing helix chain 'q' and resid 433 through 446 removed outlier: 4.254A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 456 removed outlier: 3.616A pdb=" N SER q 456 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 459 through 473 removed outlier: 3.632A pdb=" N LYS q 466 " --> pdb=" O GLU q 462 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'Z' and resid 17 through 35 Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 71 through 88 removed outlier: 3.713A pdb=" N LEU Z 76 " --> pdb=" O PRO Z 72 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE Z 77 " --> pdb=" O THR Z 73 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR Z 82 " --> pdb=" O ALA Z 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 111 Processing helix chain 'Z' and resid 115 through 137 removed outlier: 3.750A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 424 Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.165A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU Z 445 " --> pdb=" O ALA Z 441 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 455 removed outlier: 3.539A pdb=" N ALA Z 452 " --> pdb=" O PRO Z 448 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 469 removed outlier: 3.565A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'z' and resid 17 through 35 removed outlier: 3.518A pdb=" N ASN z 23 " --> pdb=" O ALA z 19 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 61 through 66 Processing helix chain 'z' and resid 71 through 88 removed outlier: 3.554A pdb=" N SER z 75 " --> pdb=" O HIS z 71 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU z 76 " --> pdb=" O PRO z 72 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE z 77 " --> pdb=" O THR z 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE z 87 " --> pdb=" O ALA z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.589A pdb=" N LEU z 108 " --> pdb=" O LYS z 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.780A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU z 135 " --> pdb=" O LEU z 131 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU z 136 " --> pdb=" O GLN z 132 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 157 removed outlier: 3.720A pdb=" N ASP z 150 " --> pdb=" O GLU z 146 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 160 No H-bonds generated for 'chain 'z' and resid 158 through 160' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.957A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.748A pdb=" N LEU z 384 " --> pdb=" O ASN z 380 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 424 Processing helix chain 'z' and resid 433 through 445 removed outlier: 3.558A pdb=" N LEU z 445 " --> pdb=" O ALA z 441 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 455 Processing helix chain 'z' and resid 458 through 469 removed outlier: 3.717A pdb=" N LEU z 463 " --> pdb=" O LEU z 459 " (cutoff:3.500A) Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 498 through 517 removed outlier: 3.590A pdb=" N VAL z 510 " --> pdb=" O HIS z 506 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'a' and resid 10 through 13 removed outlier: 6.363A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 44 through 46 Processing sheet with id=AA3, first strand: chain 'a' and resid 137 through 138 removed outlier: 3.622A pdb=" N ILE a 137 " --> pdb=" O VAL a 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.575A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 11 through 13 removed outlier: 4.717A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 61 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 409 through 410 Processing sheet with id=AA8, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA9, first strand: chain 'b' and resid 17 through 18 removed outlier: 6.140A pdb=" N ASP e 56 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASN b 519 " --> pdb=" O ASP e 56 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 62 through 64 removed outlier: 6.444A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 406 through 407 Processing sheet with id=AB3, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 18 removed outlier: 4.473A pdb=" N VAL B 517 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N MET E 58 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN B 519 " --> pdb=" O MET E 58 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL E 60 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ILE B 521 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.638A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'D' and resid 421 through 423 Processing sheet with id=AB8, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.819A pdb=" N GLY D 492 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 421 through 423 Processing sheet with id=AC1, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AC2, first strand: chain 'E' and resid 417 through 418 Processing sheet with id=AC3, first strand: chain 'E' and resid 531 through 532 removed outlier: 7.061A pdb=" N ARG E 532 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 23 through 27 removed outlier: 3.529A pdb=" N LYS e 533 " --> pdb=" O SER e 24 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU e 26 " --> pdb=" O ILE e 531 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE e 531 " --> pdb=" O LEU e 26 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE e 528 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU h 48 " --> pdb=" O ILE e 528 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP e 530 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL h 50 " --> pdb=" O ASP e 530 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG e 532 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'e' and resid 416 through 418 Processing sheet with id=AC6, first strand: chain 'g' and resid 57 through 58 removed outlier: 6.626A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE z 521 " --> pdb=" O ALA z 14 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA z 14 " --> pdb=" O ILE z 521 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 58 removed outlier: 3.831A pdb=" N VAL G 58 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU G 50 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC9, first strand: chain 'h' and resid 15 through 17 removed outlier: 4.101A pdb=" N SER h 16 " --> pdb=" O THR h 519 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR h 519 " --> pdb=" O SER h 16 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AD2, first strand: chain 'h' and resid 197 through 200 Processing sheet with id=AD3, first strand: chain 'h' and resid 475 through 477 Processing sheet with id=AD4, first strand: chain 'H' and resid 16 through 17 removed outlier: 4.146A pdb=" N SER H 16 " --> pdb=" O THR H 519 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR H 519 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 406 through 407 Processing sheet with id=AD6, first strand: chain 'H' and resid 475 through 477 Processing sheet with id=AD7, first strand: chain 'Q' and resid 409 through 410 Processing sheet with id=AD8, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AD9, first strand: chain 'Q' and resid 521 through 526 removed outlier: 4.677A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Z 45 " --> pdb=" O THR Z 57 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'q' and resid 408 through 410 Processing sheet with id=AE2, first strand: chain 'q' and resid 478 through 480 removed outlier: 3.530A pdb=" N LYS q 490 " --> pdb=" O GLY q 479 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'q' and resid 521 through 526 removed outlier: 4.713A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id=AE5, first strand: chain 'Z' and resid 478 through 479 Processing sheet with id=AE6, first strand: chain 'z' and resid 407 through 409 Processing sheet with id=AE7, first strand: chain 'z' and resid 477 through 479 2162 hydrogen bonds defined for protein. 6366 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: 6.65 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11527 1.35 - 1.47: 6451 1.47 - 1.59: 15947 1.59 - 1.71: 18 1.71 - 1.83: 330 Bond restraints: 34273 Sorted by residual: bond pdb=" C ASN A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.331 1.346 -0.015 7.90e-03 1.60e+04 3.49e+00 bond pdb=" CA PHE b 12 " pdb=" CB PHE b 12 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.35e-02 5.49e+03 1.49e+00 bond pdb=" N GLY A 9 " pdb=" CA GLY A 9 " ideal model delta sigma weight residual 1.453 1.443 0.010 8.60e-03 1.35e+04 1.36e+00 bond pdb=" C LEU Z 7 " pdb=" N ASN Z 8 " ideal model delta sigma weight residual 1.327 1.358 -0.031 2.86e-02 1.22e+03 1.21e+00 bond pdb=" C VAL G 408 " pdb=" N PRO G 409 " ideal model delta sigma weight residual 1.335 1.344 -0.009 8.70e-03 1.32e+04 1.17e+00 ... (remaining 34268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 45090 1.23 - 2.47: 951 2.47 - 3.70: 115 3.70 - 4.94: 97 4.94 - 6.17: 68 Bond angle restraints: 46321 Sorted by residual: angle pdb=" N ILE G 495 " pdb=" CA ILE G 495 " pdb=" C ILE G 495 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N ILE g 495 " pdb=" CA ILE g 495 " pdb=" C ILE g 495 " ideal model delta sigma weight residual 111.91 108.69 3.22 8.90e-01 1.26e+00 1.31e+01 angle pdb=" N VAL Z 429 " pdb=" CA VAL Z 429 " pdb=" C VAL Z 429 " ideal model delta sigma weight residual 112.12 109.33 2.79 8.40e-01 1.42e+00 1.10e+01 angle pdb=" N VAL e 153 " pdb=" CA VAL e 153 " pdb=" C VAL e 153 " ideal model delta sigma weight residual 111.62 109.25 2.37 7.90e-01 1.60e+00 9.00e+00 angle pdb=" C VAL e 155 " pdb=" N ASP e 156 " pdb=" CA ASP e 156 " ideal model delta sigma weight residual 121.54 126.75 -5.21 1.91e+00 2.74e-01 7.45e+00 ... (remaining 46316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.20: 20408 22.20 - 44.40: 693 44.40 - 66.60: 65 66.60 - 88.80: 13 88.80 - 111.01: 7 Dihedral angle restraints: 21186 sinusoidal: 8353 harmonic: 12833 Sorted by residual: dihedral pdb=" O1B ADP Q 601 " pdb=" O3A ADP Q 601 " pdb=" PB ADP Q 601 " pdb=" PA ADP Q 601 " ideal model delta sinusoidal sigma weight residual -60.00 -171.01 111.01 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O1B ADP Z 601 " pdb=" O3A ADP Z 601 " pdb=" PB ADP Z 601 " pdb=" PA ADP Z 601 " ideal model delta sinusoidal sigma weight residual -60.00 -171.01 111.00 1 2.00e+01 2.50e-03 3.26e+01 dihedral pdb=" O1B ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PB ADP z 601 " pdb=" PA ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 -171.00 110.99 1 2.00e+01 2.50e-03 3.26e+01 ... (remaining 21183 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3869 0.030 - 0.059: 1083 0.059 - 0.089: 397 0.089 - 0.118: 211 0.118 - 0.148: 57 Chirality restraints: 5617 Sorted by residual: chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA VAL a 409 " pdb=" N VAL a 409 " pdb=" C VAL a 409 " pdb=" CB VAL a 409 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA ILE a 112 " pdb=" N ILE a 112 " pdb=" C ILE a 112 " pdb=" CB ILE a 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 5614 not shown) Planarity restraints: 5931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 428 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO B 429 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 429 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 429 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN e 484 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO e 485 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO e 485 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO e 485 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR b 428 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO b 429 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO b 429 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 429 " 0.024 5.00e-02 4.00e+02 ... (remaining 5928 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 41 2.32 - 2.96: 14252 2.96 - 3.61: 50800 3.61 - 4.25: 78002 4.25 - 4.90: 128929 Nonbonded interactions: 272024 Sorted by model distance: nonbonded pdb=" OD1 ASP G 93 " pdb=" O3A ADP G 601 " model vdw 1.675 3.040 nonbonded pdb=" NZ LYS e 527 " pdb=" OE2 GLU h 384 " model vdw 1.679 3.120 nonbonded pdb=" OD2 ASP G 93 " pdb=" O1A ADP G 601 " model vdw 1.682 3.040 nonbonded pdb=" OD1 ASP g 93 " pdb=" O3A ADP g 601 " model vdw 1.689 3.040 nonbonded pdb=" OD1 ASP g 93 " pdb=" O1A ADP g 601 " model vdw 1.863 3.040 ... (remaining 272019 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 'a' and (resid 5 through 133 or resid 408 through 533)) } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 24 through 151 or resid 418 through 539)) } ncs_group { reference = (chain 'G' and (resid 15 through 139 or resid 413 through 601)) selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 29.760 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 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 0.570 34276 Z= 0.369 Angle : 0.531 6.171 46321 Z= 0.269 Chirality : 0.038 0.148 5617 Planarity : 0.003 0.046 5931 Dihedral : 11.382 111.005 12862 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.10), residues: 4407 helix: -2.43 (0.07), residues: 2835 sheet: -1.66 (0.36), residues: 172 loop : -1.90 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 398 TYR 0.006 0.001 TYR g 437 PHE 0.014 0.001 PHE G 112 TRP 0.003 0.000 TRP g 478 HIS 0.002 0.000 HIS q 59 Details of bonding type rmsd covalent geometry : bond 0.00280 (34273) covalent geometry : angle 0.53130 (46321) hydrogen bonds : bond 0.26836 ( 2162) hydrogen bonds : angle 8.12817 ( 6366) Misc. bond : bond 0.36802 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1667 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 146 ASP cc_start: 0.4141 (t0) cc_final: 0.3928 (t0) REVERT: a 460 SER cc_start: 0.8396 (p) cc_final: 0.8001 (t) REVERT: A 20 GLN cc_start: 0.8650 (mt0) cc_final: 0.8313 (mt0) REVERT: A 52 VAL cc_start: 0.7776 (p) cc_final: 0.7561 (t) REVERT: A 489 ASP cc_start: 0.1888 (t0) cc_final: 0.1252 (t70) REVERT: b 97 ASP cc_start: 0.5663 (t0) cc_final: 0.5054 (m-30) REVERT: b 120 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7735 (mmtm) REVERT: b 485 ILE cc_start: 0.5865 (mt) cc_final: 0.5306 (mt) REVERT: B 52 LEU cc_start: 0.8154 (mt) cc_final: 0.7687 (mt) REVERT: B 448 THR cc_start: 0.7941 (m) cc_final: 0.7297 (p) REVERT: B 452 ASP cc_start: 0.6536 (m-30) cc_final: 0.6158 (m-30) REVERT: B 522 LYS cc_start: 0.8397 (mttt) cc_final: 0.8007 (ptpt) REVERT: D 57 MET cc_start: 0.8455 (mmm) cc_final: 0.7673 (mmm) REVERT: D 460 VAL cc_start: 0.7996 (p) cc_final: 0.7664 (t) REVERT: E 58 MET cc_start: 0.8563 (ttm) cc_final: 0.8235 (ttm) REVERT: E 71 ASP cc_start: 0.7607 (t70) cc_final: 0.7385 (t0) REVERT: E 82 ASP cc_start: 0.7062 (m-30) cc_final: 0.6841 (m-30) REVERT: E 98 ASP cc_start: 0.7333 (m-30) cc_final: 0.6907 (m-30) REVERT: E 474 GLU cc_start: 0.5689 (mt-10) cc_final: 0.5199 (mt-10) REVERT: e 32 LEU cc_start: 0.8322 (mt) cc_final: 0.7897 (tp) REVERT: e 87 LYS cc_start: 0.8549 (mttt) cc_final: 0.7563 (mttp) REVERT: g 48 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7210 (mmtm) REVERT: G 145 ASP cc_start: 0.7023 (t0) cc_final: 0.6603 (m-30) REVERT: G 449 ARG cc_start: 0.6845 (ttm170) cc_final: 0.6551 (ttm110) REVERT: G 495 ILE cc_start: 0.7471 (mm) cc_final: 0.6869 (mm) REVERT: h 46 ASP cc_start: 0.7525 (m-30) cc_final: 0.7298 (m-30) REVERT: h 49 ILE cc_start: 0.8973 (mt) cc_final: 0.8671 (mm) REVERT: h 57 THR cc_start: 0.8748 (m) cc_final: 0.8501 (p) REVERT: h 77 LYS cc_start: 0.8245 (mttt) cc_final: 0.8010 (mttm) REVERT: h 197 ILE cc_start: 0.6173 (mt) cc_final: 0.5970 (mm) REVERT: H 51 ASP cc_start: 0.5728 (p0) cc_final: 0.5182 (p0) REVERT: H 95 THR cc_start: 0.7969 (m) cc_final: 0.7707 (p) REVERT: H 135 LYS cc_start: 0.8459 (tptt) cc_final: 0.8190 (tptm) REVERT: H 452 ASN cc_start: 0.7630 (m-40) cc_final: 0.7150 (m-40) REVERT: H 481 ASN cc_start: 0.6902 (t0) cc_final: 0.6639 (t0) REVERT: H 484 ILE cc_start: 0.8132 (pt) cc_final: 0.7804 (pt) REVERT: H 521 LYS cc_start: 0.8116 (tttt) cc_final: 0.7674 (ttpp) REVERT: Q 446 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6866 (mt-10) REVERT: Q 505 TYR cc_start: 0.7401 (t80) cc_final: 0.6899 (t80) REVERT: q 30 TYR cc_start: 0.7532 (m-10) cc_final: 0.7310 (m-10) REVERT: q 31 ARG cc_start: 0.8095 (mmt180) cc_final: 0.7755 (mmt-90) REVERT: q 34 GLN cc_start: 0.8259 (tp40) cc_final: 0.8037 (mm110) REVERT: Z 432 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7492 (mtm180) REVERT: Z 460 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7353 (mm-40) REVERT: Z 507 SER cc_start: 0.8452 (t) cc_final: 0.8178 (t) REVERT: z 23 ASN cc_start: 0.8165 (m-40) cc_final: 0.7589 (m110) REVERT: z 37 ASN cc_start: 0.8115 (p0) cc_final: 0.7849 (p0) REVERT: z 66 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7688 (mt-10) REVERT: z 414 VAL cc_start: 0.8602 (t) cc_final: 0.8352 (m) REVERT: z 453 GLN cc_start: 0.7904 (mt0) cc_final: 0.7222 (mt0) REVERT: z 518 VAL cc_start: 0.8797 (t) cc_final: 0.8556 (m) outliers start: 2 outliers final: 0 residues processed: 1667 average time/residue: 0.2298 time to fit residues: 585.0642 Evaluate side-chains 874 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 874 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 3.9990 chunk 424 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 150 ASN a 450 ASN A 472 ASN A 475 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 HIS b 174 HIS b 175 HIS b 464 GLN ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN D 37 ASN D 85 HIS D 98 GLN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN E 443 GLN E 497 ASN ** E 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS g 472 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN ** H 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 175 ASN q 477 ASN Z 61 ASN Z 132 GLN Z 434 GLN z 382 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.137194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.122422 restraints weight = 73708.759| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 3.34 r_work: 0.3747 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34276 Z= 0.164 Angle : 0.651 9.577 46321 Z= 0.332 Chirality : 0.043 0.233 5617 Planarity : 0.004 0.055 5931 Dihedral : 5.064 106.101 4773 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.02 % Allowed : 14.67 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4407 helix: 0.35 (0.09), residues: 2901 sheet: -1.18 (0.35), residues: 192 loop : -1.51 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG e 181 TYR 0.020 0.002 TYR h 419 PHE 0.023 0.002 PHE a 516 TRP 0.015 0.001 TRP z 495 HIS 0.007 0.001 HIS H 468 Details of bonding type rmsd covalent geometry : bond 0.00354 (34273) covalent geometry : angle 0.65058 (46321) hydrogen bonds : bond 0.05051 ( 2162) hydrogen bonds : angle 4.44064 ( 6366) Misc. bond : bond 0.00213 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 995 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 108 VAL cc_start: 0.8879 (t) cc_final: 0.8624 (m) REVERT: a 424 GLU cc_start: 0.8681 (tt0) cc_final: 0.8376 (tt0) REVERT: a 473 GLU cc_start: 0.8583 (tp30) cc_final: 0.8007 (tp30) REVERT: a 527 ILE cc_start: 0.9009 (mm) cc_final: 0.8625 (mt) REVERT: a 528 ASP cc_start: 0.8236 (p0) cc_final: 0.7991 (p0) REVERT: A 475 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7925 (mm-40) REVERT: A 528 ASP cc_start: 0.8693 (p0) cc_final: 0.8452 (p0) REVERT: b 78 ASN cc_start: 0.8109 (t0) cc_final: 0.7885 (t0) REVERT: b 82 LYS cc_start: 0.9257 (ttmm) cc_final: 0.8881 (mtmm) REVERT: b 97 ASP cc_start: 0.6438 (t0) cc_final: 0.5281 (m-30) REVERT: b 120 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8531 (mmtm) REVERT: b 452 ASP cc_start: 0.8549 (m-30) cc_final: 0.8004 (m-30) REVERT: b 458 SER cc_start: 0.8506 (p) cc_final: 0.7813 (t) REVERT: b 478 LEU cc_start: 0.7044 (tt) cc_final: 0.6836 (tt) REVERT: b 488 MET cc_start: 0.7074 (mmm) cc_final: 0.6871 (mmm) REVERT: B 91 GLN cc_start: 0.7320 (tp-100) cc_final: 0.6937 (tp40) REVERT: B 120 LYS cc_start: 0.8942 (tttt) cc_final: 0.8721 (mptt) REVERT: B 124 GLN cc_start: 0.8391 (tp40) cc_final: 0.8095 (mm-40) REVERT: B 417 MET cc_start: 0.7896 (mtt) cc_final: 0.7662 (mpp) REVERT: B 448 THR cc_start: 0.8968 (m) cc_final: 0.8146 (p) REVERT: B 452 ASP cc_start: 0.8094 (m-30) cc_final: 0.7405 (m-30) REVERT: B 457 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8066 (p0) REVERT: B 502 GLN cc_start: 0.8649 (tp40) cc_final: 0.8391 (tp40) REVERT: B 522 LYS cc_start: 0.8302 (mttt) cc_final: 0.8060 (ptpp) REVERT: D 57 MET cc_start: 0.8907 (mmm) cc_final: 0.8299 (mmm) REVERT: D 122 LYS cc_start: 0.9173 (tptm) cc_final: 0.8913 (tptp) REVERT: D 472 ASN cc_start: 0.8333 (t0) cc_final: 0.8047 (t0) REVERT: d 46 ASP cc_start: 0.8588 (m-30) cc_final: 0.8375 (m-30) REVERT: d 138 GLN cc_start: 0.8239 (tp40) cc_final: 0.7878 (tp40) REVERT: d 446 MET cc_start: 0.8285 (mmm) cc_final: 0.7868 (mmm) REVERT: d 520 THR cc_start: 0.9125 (m) cc_final: 0.8885 (p) REVERT: E 79 MET cc_start: 0.8285 (tpp) cc_final: 0.8023 (tpt) REVERT: E 117 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8117 (mm-30) REVERT: E 120 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: e 116 GLU cc_start: 0.8672 (tt0) cc_final: 0.8360 (tp30) REVERT: e 120 GLN cc_start: 0.8215 (mp10) cc_final: 0.7992 (mp10) REVERT: e 458 MET cc_start: 0.8889 (ttm) cc_final: 0.8371 (ttm) REVERT: e 531 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8955 (mm) REVERT: e 533 LYS cc_start: 0.7735 (tptm) cc_final: 0.7420 (tptm) REVERT: g 69 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7783 (mm-30) REVERT: G 35 ASP cc_start: 0.8228 (m-30) cc_final: 0.8010 (m-30) REVERT: G 47 MET cc_start: 0.8700 (mmm) cc_final: 0.8197 (mmm) REVERT: G 87 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8120 (tm-30) REVERT: G 145 ASP cc_start: 0.7609 (t0) cc_final: 0.6919 (m-30) REVERT: G 515 LEU cc_start: 0.8628 (tt) cc_final: 0.8409 (mt) REVERT: h 21 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7166 (mm110) REVERT: h 49 ILE cc_start: 0.8998 (mt) cc_final: 0.8569 (tt) REVERT: h 51 ASP cc_start: 0.7423 (p0) cc_final: 0.7065 (p0) REVERT: h 57 THR cc_start: 0.9166 (m) cc_final: 0.8965 (p) REVERT: h 61 ASP cc_start: 0.7620 (t70) cc_final: 0.7299 (t70) REVERT: h 105 LEU cc_start: 0.9272 (mt) cc_final: 0.8992 (mt) REVERT: h 169 SER cc_start: 0.7322 (p) cc_final: 0.7010 (t) REVERT: h 443 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8070 (mt-10) REVERT: h 517 ASP cc_start: 0.7517 (t0) cc_final: 0.7019 (t0) REVERT: H 87 ASP cc_start: 0.7070 (t0) cc_final: 0.6829 (t0) REVERT: H 106 LYS cc_start: 0.8623 (tttp) cc_final: 0.8211 (ttpt) REVERT: H 455 PHE cc_start: 0.7899 (m-10) cc_final: 0.7637 (m-10) REVERT: H 481 ASN cc_start: 0.7512 (t0) cc_final: 0.7298 (t0) REVERT: H 515 SER cc_start: 0.9171 (p) cc_final: 0.8575 (p) REVERT: Q 14 MET cc_start: 0.4936 (ppp) cc_final: 0.3798 (ptt) REVERT: Q 38 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8363 (pt0) REVERT: Q 468 TYR cc_start: 0.9084 (m-10) cc_final: 0.8819 (m-10) REVERT: Q 505 TYR cc_start: 0.8216 (t80) cc_final: 0.7623 (t80) REVERT: q 31 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8195 (mpt180) REVERT: q 52 MET cc_start: 0.8972 (mmm) cc_final: 0.8570 (mmm) REVERT: q 73 LEU cc_start: 0.9157 (mt) cc_final: 0.8886 (mt) REVERT: q 75 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7288 (mm-30) REVERT: q 88 MET cc_start: 0.8222 (mtp) cc_final: 0.7919 (mmm) REVERT: q 114 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8801 (mm) REVERT: q 118 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8456 (mm) REVERT: q 390 ARG cc_start: 0.9125 (ptp90) cc_final: 0.8862 (ptp90) REVERT: q 523 GLN cc_start: 0.8467 (tt0) cc_final: 0.8260 (tp40) REVERT: Z 35 ARG cc_start: 0.8003 (ptt90) cc_final: 0.7597 (ptp-170) REVERT: Z 121 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: Z 128 GLU cc_start: 0.8084 (tp30) cc_final: 0.7867 (tp30) REVERT: Z 135 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7542 (mm-30) REVERT: z 520 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7533 (mm-30) outliers start: 110 outliers final: 47 residues processed: 1058 average time/residue: 0.2039 time to fit residues: 345.1083 Evaluate side-chains 852 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 797 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 475 GLN Chi-restraints excluded: chain b residue 51 ILE Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 46 MET Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 120 GLN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 531 ILE Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 513 ASN Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 166 THR Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 30 LEU Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 121 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 483 THR Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 520 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 346 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 228 optimal weight: 0.7980 chunk 121 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 220 optimal weight: 10.0000 chunk 387 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 423 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 443 GLN g 111 HIS G 453 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 448 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN H 462 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 435 GLN Z 61 ASN Z 115 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.134639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.119348 restraints weight = 73864.873| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 3.37 r_work: 0.3701 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34276 Z= 0.137 Angle : 0.600 7.696 46321 Z= 0.300 Chirality : 0.042 0.198 5617 Planarity : 0.004 0.051 5931 Dihedral : 4.774 101.505 4773 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.21 % Allowed : 16.81 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 4407 helix: 1.22 (0.09), residues: 2892 sheet: -0.58 (0.36), residues: 180 loop : -1.23 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG h 37 TYR 0.013 0.001 TYR H 475 PHE 0.013 0.001 PHE D 137 TRP 0.007 0.001 TRP g 435 HIS 0.016 0.001 HIS z 161 Details of bonding type rmsd covalent geometry : bond 0.00306 (34273) covalent geometry : angle 0.59953 (46321) hydrogen bonds : bond 0.04242 ( 2162) hydrogen bonds : angle 4.02218 ( 6366) Misc. bond : bond 0.00068 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 904 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 GLN cc_start: 0.9169 (mt0) cc_final: 0.8513 (mm-40) REVERT: a 108 VAL cc_start: 0.8920 (t) cc_final: 0.8645 (m) REVERT: a 430 MET cc_start: 0.8137 (mtp) cc_final: 0.7853 (mtp) REVERT: a 443 ARG cc_start: 0.8868 (mtm110) cc_final: 0.8516 (ttp-110) REVERT: a 527 ILE cc_start: 0.8994 (mm) cc_final: 0.8691 (mt) REVERT: A 51 ASP cc_start: 0.6857 (m-30) cc_final: 0.6570 (m-30) REVERT: A 106 GLU cc_start: 0.7789 (pt0) cc_final: 0.7398 (pt0) REVERT: A 109 LYS cc_start: 0.8998 (mmtp) cc_final: 0.8731 (mmtp) REVERT: A 110 GLN cc_start: 0.8505 (mp10) cc_final: 0.8115 (mp10) REVERT: A 131 TYR cc_start: 0.8611 (t80) cc_final: 0.8254 (t80) REVERT: A 473 GLU cc_start: 0.8211 (tp30) cc_final: 0.7986 (tp30) REVERT: b 29 PHE cc_start: 0.8043 (m-10) cc_final: 0.7786 (m-10) REVERT: b 49 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7781 (t0) REVERT: b 63 VAL cc_start: 0.9032 (t) cc_final: 0.8829 (p) REVERT: b 97 ASP cc_start: 0.6463 (t0) cc_final: 0.5418 (m-30) REVERT: b 120 LYS cc_start: 0.9135 (mtmt) cc_final: 0.8662 (mmtm) REVERT: b 142 LEU cc_start: 0.8746 (tp) cc_final: 0.8458 (tp) REVERT: b 162 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7791 (tt) REVERT: b 458 SER cc_start: 0.8561 (p) cc_final: 0.8210 (t) REVERT: b 478 LEU cc_start: 0.7189 (tt) cc_final: 0.6914 (tt) REVERT: b 502 GLN cc_start: 0.8115 (mt0) cc_final: 0.7793 (mt0) REVERT: B 91 GLN cc_start: 0.7474 (tp-100) cc_final: 0.7091 (tp40) REVERT: B 108 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8546 (mm-30) REVERT: B 120 LYS cc_start: 0.9076 (tttt) cc_final: 0.8836 (mptt) REVERT: B 448 THR cc_start: 0.9282 (m) cc_final: 0.8838 (p) REVERT: D 57 MET cc_start: 0.8870 (mmm) cc_final: 0.8273 (mmm) REVERT: D 96 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8448 (mtmt) REVERT: d 46 ASP cc_start: 0.8714 (m-30) cc_final: 0.8476 (m-30) REVERT: d 138 GLN cc_start: 0.8375 (tp40) cc_final: 0.7896 (tp40) REVERT: d 446 MET cc_start: 0.8318 (mmm) cc_final: 0.7895 (mmm) REVERT: d 520 THR cc_start: 0.9159 (m) cc_final: 0.8935 (p) REVERT: E 37 MET cc_start: 0.8583 (mmp) cc_final: 0.8361 (mmp) REVERT: E 79 MET cc_start: 0.8289 (tpp) cc_final: 0.7761 (tpt) REVERT: E 117 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8256 (mm-30) REVERT: E 444 TYR cc_start: 0.8111 (m-80) cc_final: 0.7825 (m-80) REVERT: e 80 ASP cc_start: 0.7360 (p0) cc_final: 0.6951 (t0) REVERT: e 89 MET cc_start: 0.8446 (mtm) cc_final: 0.8155 (mtp) REVERT: e 116 GLU cc_start: 0.8567 (tt0) cc_final: 0.8322 (tp30) REVERT: e 120 GLN cc_start: 0.8262 (mp10) cc_final: 0.8025 (mp10) REVERT: e 391 MET cc_start: 0.7173 (mpp) cc_final: 0.6896 (ppp) REVERT: e 393 ILE cc_start: 0.6658 (mt) cc_final: 0.6348 (tt) REVERT: e 442 GLU cc_start: 0.7592 (tt0) cc_final: 0.7362 (tt0) REVERT: e 463 ASN cc_start: 0.8820 (m-40) cc_final: 0.8411 (m110) REVERT: e 533 LYS cc_start: 0.7700 (tptm) cc_final: 0.7354 (tptm) REVERT: g 38 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8352 (mtp85) REVERT: g 69 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7846 (mm-30) REVERT: g 124 SER cc_start: 0.9366 (m) cc_final: 0.9115 (p) REVERT: g 132 ASP cc_start: 0.7960 (m-30) cc_final: 0.7500 (m-30) REVERT: g 503 LEU cc_start: 0.8913 (mt) cc_final: 0.8678 (mt) REVERT: G 47 MET cc_start: 0.8835 (mmm) cc_final: 0.8009 (mmm) REVERT: G 59 MET cc_start: 0.8096 (mmm) cc_final: 0.7848 (mmm) REVERT: G 69 GLU cc_start: 0.6883 (tp30) cc_final: 0.6457 (tm-30) REVERT: G 73 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7543 (pm20) REVERT: G 145 ASP cc_start: 0.7961 (t0) cc_final: 0.7198 (m-30) REVERT: h 21 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7502 (tm-30) REVERT: h 105 LEU cc_start: 0.9299 (mt) cc_final: 0.8997 (mt) REVERT: h 394 MET cc_start: 0.8064 (mmp) cc_final: 0.7733 (mmp) REVERT: h 451 ASP cc_start: 0.8541 (m-30) cc_final: 0.7910 (m-30) REVERT: h 508 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8562 (mp0) REVERT: h 517 ASP cc_start: 0.7307 (t0) cc_final: 0.7091 (t0) REVERT: H 25 ASN cc_start: 0.9081 (m-40) cc_final: 0.8773 (m110) REVERT: H 106 LYS cc_start: 0.8605 (tttp) cc_final: 0.8211 (ttpt) REVERT: H 130 GLN cc_start: 0.8066 (mm110) cc_final: 0.7762 (tp-100) REVERT: H 415 GLU cc_start: 0.8566 (tp30) cc_final: 0.8353 (tp30) REVERT: H 455 PHE cc_start: 0.7973 (m-10) cc_final: 0.7762 (m-10) REVERT: H 497 MET cc_start: 0.7867 (ppp) cc_final: 0.7560 (ppp) REVERT: H 501 ASN cc_start: 0.8165 (m-40) cc_final: 0.7881 (m-40) REVERT: Q 14 MET cc_start: 0.4532 (ppp) cc_final: 0.3573 (ptt) REVERT: Q 38 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8340 (pt0) REVERT: Q 117 GLU cc_start: 0.8449 (tp30) cc_final: 0.8228 (tp30) REVERT: Q 468 TYR cc_start: 0.9103 (m-10) cc_final: 0.8831 (m-10) REVERT: q 27 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6452 (mt-10) REVERT: q 34 GLN cc_start: 0.8226 (tp40) cc_final: 0.7976 (mm-40) REVERT: q 41 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8133 (mm-40) REVERT: q 114 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8746 (mm) REVERT: q 385 MET cc_start: 0.4518 (mtt) cc_final: 0.3488 (ttt) REVERT: q 523 GLN cc_start: 0.8455 (tt0) cc_final: 0.8233 (tp40) REVERT: Z 35 ARG cc_start: 0.8215 (ptt90) cc_final: 0.7926 (ptp-170) REVERT: Z 121 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7756 (mp0) REVERT: Z 420 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7288 (mm-30) REVERT: Z 453 GLN cc_start: 0.9255 (mt0) cc_final: 0.8797 (mt0) REVERT: Z 458 ASP cc_start: 0.7926 (t0) cc_final: 0.7124 (t0) REVERT: Z 467 GLN cc_start: 0.8853 (tt0) cc_final: 0.8474 (mm-40) REVERT: Z 514 ASN cc_start: 0.8880 (m-40) cc_final: 0.8247 (t0) REVERT: Z 520 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7799 (tm-30) REVERT: Z 526 MET cc_start: 0.3192 (ttt) cc_final: 0.2593 (tmm) REVERT: z 23 ASN cc_start: 0.8501 (m-40) cc_final: 0.8136 (m-40) REVERT: z 37 ASN cc_start: 0.8993 (p0) cc_final: 0.8729 (p0) REVERT: z 46 MET cc_start: 0.7865 (ttm) cc_final: 0.7495 (ttm) REVERT: z 99 ILE cc_start: 0.8965 (mt) cc_final: 0.8597 (mm) REVERT: z 520 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8094 (mm-30) outliers start: 117 outliers final: 65 residues processed: 971 average time/residue: 0.2003 time to fit residues: 313.4857 Evaluate side-chains 816 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 745 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 65 LEU Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 529 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain g residue 33 ILE Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 388 SER Chi-restraints excluded: chain h residue 448 GLN Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain h residue 512 LEU Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 518 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 153 ASN Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 30 LEU Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 121 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 76 LEU Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 507 SER Chi-restraints excluded: chain z residue 520 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 154 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 300 optimal weight: 0.9990 chunk 247 optimal weight: 0.1980 chunk 425 optimal weight: 3.9990 chunk 181 optimal weight: 0.0670 chunk 31 optimal weight: 10.0000 chunk 293 optimal weight: 2.9990 overall best weight: 1.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 435 GLN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 23 GLN g 111 HIS h 30 GLN ** h 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN H 107 GLN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN q 140 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.133069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.118237 restraints weight = 73720.558| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 3.31 r_work: 0.3679 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34276 Z= 0.130 Angle : 0.594 10.008 46321 Z= 0.294 Chirality : 0.041 0.227 5617 Planarity : 0.003 0.046 5931 Dihedral : 4.593 99.897 4773 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.99 % Allowed : 18.13 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.02 (0.12), residues: 4407 helix: 1.57 (0.09), residues: 2893 sheet: -0.50 (0.34), residues: 201 loop : -1.11 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG z 28 TYR 0.018 0.001 TYR a 426 PHE 0.010 0.001 PHE q 178 TRP 0.006 0.001 TRP g 435 HIS 0.010 0.001 HIS z 161 Details of bonding type rmsd covalent geometry : bond 0.00288 (34273) covalent geometry : angle 0.59393 (46321) hydrogen bonds : bond 0.03864 ( 2162) hydrogen bonds : angle 3.86074 ( 6366) Misc. bond : bond 0.00107 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 855 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 GLN cc_start: 0.9116 (mt0) cc_final: 0.8463 (mm-40) REVERT: a 443 ARG cc_start: 0.8931 (mtm110) cc_final: 0.8472 (ttp-110) REVERT: a 527 ILE cc_start: 0.8991 (mm) cc_final: 0.8711 (mt) REVERT: A 51 ASP cc_start: 0.6926 (m-30) cc_final: 0.6649 (m-30) REVERT: A 106 GLU cc_start: 0.7816 (pt0) cc_final: 0.7612 (pt0) REVERT: A 109 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8939 (mmtp) REVERT: A 466 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8069 (mtmm) REVERT: A 473 GLU cc_start: 0.8314 (tp30) cc_final: 0.7986 (tp30) REVERT: b 49 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7532 (t0) REVERT: b 82 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8669 (tptp) REVERT: b 97 ASP cc_start: 0.6477 (t0) cc_final: 0.5146 (m-30) REVERT: b 120 LYS cc_start: 0.9312 (mtmt) cc_final: 0.8890 (mmtm) REVERT: b 142 LEU cc_start: 0.8934 (tp) cc_final: 0.8613 (tp) REVERT: b 162 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8113 (tt) REVERT: b 437 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7138 (tm-30) REVERT: b 441 LYS cc_start: 0.8688 (mptt) cc_final: 0.8120 (mptt) REVERT: b 445 MET cc_start: 0.8342 (mmp) cc_final: 0.8136 (mmp) REVERT: b 458 SER cc_start: 0.8679 (p) cc_final: 0.8180 (t) REVERT: b 480 MET cc_start: 0.7308 (pmm) cc_final: 0.6813 (mmm) REVERT: B 77 ASP cc_start: 0.7292 (p0) cc_final: 0.6218 (m-30) REVERT: B 91 GLN cc_start: 0.7592 (tp-100) cc_final: 0.7212 (tp40) REVERT: B 108 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8552 (mm-30) REVERT: B 448 THR cc_start: 0.9345 (m) cc_final: 0.8911 (p) REVERT: B 522 LYS cc_start: 0.8179 (mttt) cc_final: 0.7866 (ptpp) REVERT: D 57 MET cc_start: 0.8926 (mmm) cc_final: 0.8625 (mmt) REVERT: D 459 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8472 (mm-30) REVERT: d 46 ASP cc_start: 0.8864 (m-30) cc_final: 0.8618 (m-30) REVERT: d 82 GLN cc_start: 0.7721 (pt0) cc_final: 0.7343 (tm-30) REVERT: d 138 GLN cc_start: 0.8531 (tp40) cc_final: 0.8153 (tp40) REVERT: d 520 THR cc_start: 0.9154 (m) cc_final: 0.8925 (p) REVERT: E 37 MET cc_start: 0.8564 (mmp) cc_final: 0.8345 (mmp) REVERT: E 46 MET cc_start: 0.8390 (mtp) cc_final: 0.8004 (ttt) REVERT: E 79 MET cc_start: 0.8349 (tpp) cc_final: 0.7622 (tpt) REVERT: E 117 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8412 (mm-30) REVERT: e 30 GLU cc_start: 0.8702 (mp0) cc_final: 0.7946 (pp20) REVERT: e 116 GLU cc_start: 0.8664 (tt0) cc_final: 0.8390 (tt0) REVERT: e 120 GLN cc_start: 0.8323 (mp10) cc_final: 0.8109 (mp10) REVERT: e 442 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: e 463 ASN cc_start: 0.8828 (m-40) cc_final: 0.8498 (m-40) REVERT: e 533 LYS cc_start: 0.7620 (tptm) cc_final: 0.7258 (tptm) REVERT: g 38 ARG cc_start: 0.8713 (mmm-85) cc_final: 0.8512 (mtp85) REVERT: g 69 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7910 (mm-30) REVERT: g 124 SER cc_start: 0.9388 (m) cc_final: 0.9149 (p) REVERT: g 454 ASN cc_start: 0.9142 (m-40) cc_final: 0.8753 (m-40) REVERT: g 518 ARG cc_start: 0.8451 (mtp85) cc_final: 0.7995 (mtp85) REVERT: G 47 MET cc_start: 0.8863 (mmm) cc_final: 0.8005 (mmm) REVERT: G 59 MET cc_start: 0.8217 (mmm) cc_final: 0.7938 (mmm) REVERT: G 69 GLU cc_start: 0.7080 (tp30) cc_final: 0.6727 (tm-30) REVERT: G 73 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7615 (pm20) REVERT: G 145 ASP cc_start: 0.8043 (t0) cc_final: 0.7296 (m-30) REVERT: h 21 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7516 (tm-30) REVERT: h 61 ASP cc_start: 0.8107 (t70) cc_final: 0.7752 (t70) REVERT: h 105 LEU cc_start: 0.9265 (mt) cc_final: 0.8959 (mt) REVERT: h 199 LYS cc_start: 0.5477 (tptt) cc_final: 0.5213 (tptt) REVERT: h 387 ARG cc_start: 0.7189 (ptm-80) cc_final: 0.6743 (ptm160) REVERT: h 394 MET cc_start: 0.8094 (mmp) cc_final: 0.7784 (mmp) REVERT: h 443 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8211 (mt-10) REVERT: h 475 TYR cc_start: 0.7465 (m-80) cc_final: 0.7153 (m-10) REVERT: h 497 MET cc_start: 0.8434 (mmm) cc_final: 0.7942 (mmm) REVERT: h 517 ASP cc_start: 0.7323 (t0) cc_final: 0.7036 (t0) REVERT: H 106 LYS cc_start: 0.8663 (tttp) cc_final: 0.8264 (ttpt) REVERT: H 413 GLU cc_start: 0.8584 (mp0) cc_final: 0.8329 (mm-30) REVERT: H 414 MET cc_start: 0.8704 (mmm) cc_final: 0.8451 (mmm) REVERT: H 415 GLU cc_start: 0.8547 (tp30) cc_final: 0.8221 (tp30) REVERT: Q 14 MET cc_start: 0.4318 (ppp) cc_final: 0.3508 (ptt) REVERT: Q 116 GLU cc_start: 0.8193 (tp30) cc_final: 0.7444 (tp30) REVERT: Q 120 ARG cc_start: 0.8667 (mmt90) cc_final: 0.8394 (mmt90) REVERT: Q 468 TYR cc_start: 0.9111 (m-10) cc_final: 0.8881 (m-10) REVERT: q 31 ARG cc_start: 0.8201 (mpt180) cc_final: 0.7959 (mtt90) REVERT: q 34 GLN cc_start: 0.8306 (tp40) cc_final: 0.8025 (mm110) REVERT: q 41 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8083 (tp40) REVERT: q 52 MET cc_start: 0.8994 (mmm) cc_final: 0.8784 (mmm) REVERT: q 114 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8783 (mm) REVERT: q 134 ILE cc_start: 0.9067 (mt) cc_final: 0.8846 (mm) REVERT: q 385 MET cc_start: 0.4630 (mtt) cc_final: 0.3473 (ttt) REVERT: Z 35 ARG cc_start: 0.8472 (ptt90) cc_final: 0.8178 (ptp-170) REVERT: Z 59 ASP cc_start: 0.7415 (t70) cc_final: 0.6979 (t70) REVERT: Z 121 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: Z 453 GLN cc_start: 0.9299 (mt0) cc_final: 0.8888 (mt0) REVERT: Z 462 THR cc_start: 0.9264 (m) cc_final: 0.8999 (t) REVERT: Z 514 ASN cc_start: 0.8962 (m-40) cc_final: 0.8332 (t0) REVERT: Z 520 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7706 (tm-30) REVERT: Z 521 ILE cc_start: 0.8658 (mt) cc_final: 0.8229 (mt) REVERT: z 23 ASN cc_start: 0.8464 (m-40) cc_final: 0.8106 (m-40) REVERT: z 99 ILE cc_start: 0.8961 (mt) cc_final: 0.8602 (mm) REVERT: z 458 ASP cc_start: 0.7552 (t0) cc_final: 0.7345 (t0) REVERT: z 520 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8124 (mm-30) outliers start: 109 outliers final: 59 residues processed: 920 average time/residue: 0.1992 time to fit residues: 296.8627 Evaluate side-chains 817 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 751 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 466 LYS Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 132 GLU Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 493 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 442 GLU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain g residue 22 VAL Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 80 MET Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 433 LEU Chi-restraints excluded: chain h residue 479 ILE Chi-restraints excluded: chain h residue 512 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 465 SER Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 130 GLU Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 121 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 32 ASP Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 499 CYS Chi-restraints excluded: chain z residue 520 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 330 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 417 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 440 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 429 optimal weight: 5.9990 chunk 340 optimal weight: 0.6980 chunk 134 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN a 135 ASN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 453 ASN D 37 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 GLN d 165 ASN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 453 GLN ** h 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 481 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 13 GLN q 59 HIS Z 37 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.122908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.107297 restraints weight = 78654.095| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.27 r_work: 0.3541 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.6681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34276 Z= 0.216 Angle : 0.690 10.814 46321 Z= 0.344 Chirality : 0.044 0.280 5617 Planarity : 0.004 0.062 5931 Dihedral : 5.060 93.636 4773 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.15 % Allowed : 18.21 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.13), residues: 4407 helix: 1.53 (0.09), residues: 2901 sheet: -0.15 (0.35), residues: 211 loop : -1.32 (0.16), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 467 TYR 0.024 0.002 TYR q 505 PHE 0.019 0.002 PHE q 399 TRP 0.016 0.002 TRP g 435 HIS 0.007 0.001 HIS a 113 Details of bonding type rmsd covalent geometry : bond 0.00488 (34273) covalent geometry : angle 0.68974 (46321) hydrogen bonds : bond 0.04679 ( 2162) hydrogen bonds : angle 4.07588 ( 6366) Misc. bond : bond 0.00135 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 943 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 792 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 99 GLU cc_start: 0.8243 (tp30) cc_final: 0.8014 (tp30) REVERT: a 106 GLU cc_start: 0.8079 (tp30) cc_final: 0.7695 (tp30) REVERT: a 110 GLN cc_start: 0.8981 (mt0) cc_final: 0.8586 (mt0) REVERT: a 443 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.7930 (ttp80) REVERT: a 519 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8476 (mm-30) REVERT: A 51 ASP cc_start: 0.7736 (m-30) cc_final: 0.7453 (m-30) REVERT: A 105 ASP cc_start: 0.8509 (t70) cc_final: 0.8059 (t0) REVERT: A 109 LYS cc_start: 0.9151 (mmtp) cc_final: 0.8736 (mmtp) REVERT: A 110 GLN cc_start: 0.8471 (mp10) cc_final: 0.8141 (mp10) REVERT: A 440 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 443 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.7817 (ttp-110) REVERT: A 468 ARG cc_start: 0.9110 (mtp85) cc_final: 0.8907 (mtp-110) REVERT: b 49 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7945 (t0) REVERT: b 53 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7604 (pp) REVERT: b 82 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8705 (tptp) REVERT: b 97 ASP cc_start: 0.5936 (t0) cc_final: 0.4815 (m-30) REVERT: b 120 LYS cc_start: 0.9377 (mtmt) cc_final: 0.9008 (mmtm) REVERT: b 142 LEU cc_start: 0.8753 (tp) cc_final: 0.8472 (tp) REVERT: b 162 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8468 (tt) REVERT: b 408 TYR cc_start: 0.8534 (m-80) cc_final: 0.8183 (m-10) REVERT: b 437 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7586 (tm-30) REVERT: b 441 LYS cc_start: 0.8914 (mptt) cc_final: 0.8576 (mptt) REVERT: b 453 ASN cc_start: 0.8967 (m-40) cc_final: 0.8745 (m110) REVERT: B 43 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8952 (mm) REVERT: B 82 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8449 (tttt) REVERT: B 91 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7723 (tp-100) REVERT: B 108 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8536 (mm-30) REVERT: B 452 ASP cc_start: 0.8309 (m-30) cc_final: 0.7654 (m-30) REVERT: B 512 GLU cc_start: 0.8115 (tt0) cc_final: 0.7886 (tt0) REVERT: B 522 LYS cc_start: 0.8285 (mttt) cc_final: 0.7901 (ptpp) REVERT: D 57 MET cc_start: 0.9030 (mmm) cc_final: 0.8415 (mmm) REVERT: D 82 GLN cc_start: 0.7602 (mm110) cc_final: 0.6954 (pt0) REVERT: D 138 GLN cc_start: 0.8827 (tp40) cc_final: 0.8541 (tp40) REVERT: D 459 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8353 (mm-30) REVERT: d 46 ASP cc_start: 0.8946 (m-30) cc_final: 0.8688 (m-30) REVERT: d 49 ARG cc_start: 0.8852 (ptm-80) cc_final: 0.8480 (ttp80) REVERT: E 37 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8519 (mmp) REVERT: E 79 MET cc_start: 0.8489 (tpp) cc_final: 0.7983 (tpt) REVERT: E 117 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8327 (mm-30) REVERT: E 524 MET cc_start: 0.8712 (tpp) cc_final: 0.8325 (tpp) REVERT: e 87 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8645 (mmtp) REVERT: e 442 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: e 447 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.7909 (mtm180) REVERT: e 463 ASN cc_start: 0.9024 (m-40) cc_final: 0.8608 (m110) REVERT: g 38 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8513 (mtp85) REVERT: g 69 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8063 (mm-30) REVERT: g 124 SER cc_start: 0.9394 (m) cc_final: 0.9129 (p) REVERT: G 20 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6275 (ttp80) REVERT: G 38 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.7429 (tmm-80) REVERT: G 47 MET cc_start: 0.8973 (mmm) cc_final: 0.8390 (mmm) REVERT: G 59 MET cc_start: 0.8004 (mmm) cc_final: 0.7183 (tpp) REVERT: G 69 GLU cc_start: 0.7288 (tp30) cc_final: 0.7022 (tm-30) REVERT: G 73 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7698 (pm20) REVERT: G 415 GLU cc_start: 0.8493 (mp0) cc_final: 0.7963 (mp0) REVERT: h 21 GLN cc_start: 0.8191 (tm-30) cc_final: 0.7779 (tm-30) REVERT: h 61 ASP cc_start: 0.8150 (t70) cc_final: 0.7830 (t70) REVERT: h 105 LEU cc_start: 0.9385 (mt) cc_final: 0.9044 (mt) REVERT: h 387 ARG cc_start: 0.7331 (ptm-80) cc_final: 0.6852 (ptm160) REVERT: h 394 MET cc_start: 0.7876 (mmp) cc_final: 0.7581 (mmp) REVERT: h 443 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8576 (mt-10) REVERT: h 497 MET cc_start: 0.8673 (mmm) cc_final: 0.8331 (mmm) REVERT: h 511 CYS cc_start: 0.8585 (m) cc_final: 0.8351 (m) REVERT: H 25 ASN cc_start: 0.9267 (m-40) cc_final: 0.8864 (m-40) REVERT: H 45 MET cc_start: 0.7893 (ttm) cc_final: 0.7451 (ttt) REVERT: H 96 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8480 (t) REVERT: H 106 LYS cc_start: 0.8758 (tttp) cc_final: 0.8281 (ttpt) REVERT: H 413 GLU cc_start: 0.8866 (mp0) cc_final: 0.8623 (mm-30) REVERT: H 415 GLU cc_start: 0.8914 (tp30) cc_final: 0.8452 (tp30) REVERT: H 422 ASP cc_start: 0.8749 (m-30) cc_final: 0.8245 (p0) REVERT: H 481 ASN cc_start: 0.7719 (t0) cc_final: 0.7459 (t0) REVERT: H 501 ASN cc_start: 0.8289 (m-40) cc_final: 0.8038 (m-40) REVERT: Q 14 MET cc_start: 0.4098 (ppp) cc_final: 0.3274 (ptt) REVERT: Q 38 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8309 (pt0) REVERT: Q 116 GLU cc_start: 0.7910 (tp30) cc_final: 0.7158 (tp30) REVERT: Q 468 TYR cc_start: 0.9145 (m-10) cc_final: 0.8923 (m-10) REVERT: q 31 ARG cc_start: 0.8338 (mpt180) cc_final: 0.7826 (mpt180) REVERT: q 41 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8335 (tp40) REVERT: q 114 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8817 (mm) REVERT: q 385 MET cc_start: 0.4906 (mtt) cc_final: 0.3685 (ttt) REVERT: Z 136 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: Z 442 ASP cc_start: 0.8299 (m-30) cc_final: 0.8078 (m-30) REVERT: Z 453 GLN cc_start: 0.9319 (mt0) cc_final: 0.8937 (mt0) REVERT: Z 458 ASP cc_start: 0.8191 (t0) cc_final: 0.7178 (t0) REVERT: Z 520 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7546 (tm-30) REVERT: z 23 ASN cc_start: 0.8591 (m-40) cc_final: 0.8100 (m110) REVERT: z 46 MET cc_start: 0.7995 (ttm) cc_final: 0.7790 (ttm) REVERT: z 67 MET cc_start: 0.6999 (tpt) cc_final: 0.6628 (tmm) REVERT: z 99 ILE cc_start: 0.8911 (mt) cc_final: 0.8670 (mm) REVERT: z 520 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8164 (mm-30) outliers start: 151 outliers final: 85 residues processed: 893 average time/residue: 0.2015 time to fit residues: 289.3574 Evaluate side-chains 801 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 702 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 443 ARG Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 162 ILE Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 493 ILE Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 484 ASN Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 442 GLU Chi-restraints excluded: chain g residue 31 LYS Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 501 VAL Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 433 LEU Chi-restraints excluded: chain h residue 477 VAL Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 126 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 465 SER Chi-restraints excluded: chain Q residue 518 VAL Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 32 ASP Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 61 ASN Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 406 CYS Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 505 LEU Chi-restraints excluded: chain z residue 520 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 294 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 306 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 330 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 369 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 288 optimal weight: 2.9990 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 482 ASN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS D 37 ASN D 472 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN d 82 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS e 83 HIS H 462 ASN H 487 ASN Q 140 HIS q 461 ASN Z 23 ASN Z 454 ASN Z 467 GLN z 161 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.120667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.106845 restraints weight = 74865.284| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.02 r_work: 0.3496 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.7437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 34276 Z= 0.253 Angle : 0.739 12.334 46321 Z= 0.370 Chirality : 0.046 0.260 5617 Planarity : 0.004 0.053 5931 Dihedral : 5.390 87.188 4773 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.34 % Allowed : 19.51 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4407 helix: 1.41 (0.09), residues: 2902 sheet: -0.40 (0.35), residues: 203 loop : -1.43 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG z 432 TYR 0.024 0.002 TYR q 505 PHE 0.038 0.002 PHE q 103 TRP 0.017 0.002 TRP g 435 HIS 0.007 0.001 HIS G 470 Details of bonding type rmsd covalent geometry : bond 0.00577 (34273) covalent geometry : angle 0.73926 (46321) hydrogen bonds : bond 0.04844 ( 2162) hydrogen bonds : angle 4.22447 ( 6366) Misc. bond : bond 0.00165 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 756 time to evaluate : 1.325 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 20 GLN cc_start: 0.9235 (mt0) cc_final: 0.8532 (mp10) REVERT: a 95 ILE cc_start: 0.9419 (pt) cc_final: 0.9145 (mt) REVERT: a 99 GLU cc_start: 0.8258 (tp30) cc_final: 0.7799 (tp30) REVERT: a 106 GLU cc_start: 0.8117 (tp30) cc_final: 0.7815 (tp30) REVERT: a 110 GLN cc_start: 0.8824 (mt0) cc_final: 0.8297 (mt0) REVERT: A 105 ASP cc_start: 0.8661 (t70) cc_final: 0.8268 (t0) REVERT: A 109 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8549 (mmtp) REVERT: A 458 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8108 (mp10) REVERT: b 48 MET cc_start: 0.8857 (mmp) cc_final: 0.8600 (mmm) REVERT: b 49 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8025 (t0) REVERT: b 82 LYS cc_start: 0.9246 (ttmt) cc_final: 0.8743 (tptp) REVERT: b 97 ASP cc_start: 0.6200 (t0) cc_final: 0.5963 (t0) REVERT: b 111 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.8436 (ptp-110) REVERT: b 120 LYS cc_start: 0.9496 (mtmt) cc_final: 0.9143 (mmtm) REVERT: b 408 TYR cc_start: 0.8591 (m-80) cc_final: 0.8235 (m-10) REVERT: b 441 LYS cc_start: 0.8946 (mptt) cc_final: 0.8546 (mptt) REVERT: B 43 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8999 (mm) REVERT: B 82 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8455 (tttt) REVERT: B 93 ASP cc_start: 0.7352 (m-30) cc_final: 0.7133 (m-30) REVERT: B 108 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8483 (mm-30) REVERT: B 431 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8216 (mmtt) REVERT: B 438 SER cc_start: 0.9431 (OUTLIER) cc_final: 0.9077 (p) REVERT: B 516 ARG cc_start: 0.8220 (ptp-110) cc_final: 0.7662 (ptp-110) REVERT: B 522 LYS cc_start: 0.8438 (mttt) cc_final: 0.7969 (ptpp) REVERT: D 32 GLN cc_start: 0.8529 (pt0) cc_final: 0.8072 (pt0) REVERT: D 57 MET cc_start: 0.8933 (mmm) cc_final: 0.8349 (mmm) REVERT: D 459 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8435 (mm-30) REVERT: d 49 ARG cc_start: 0.8957 (ptm-80) cc_final: 0.8631 (ttp80) REVERT: d 73 ASP cc_start: 0.8724 (t0) cc_final: 0.8431 (t0) REVERT: d 82 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7782 (pp30) REVERT: d 446 MET cc_start: 0.8507 (mtp) cc_final: 0.8281 (mtp) REVERT: d 481 ARG cc_start: 0.9094 (ttp-110) cc_final: 0.8795 (ttp-170) REVERT: E 56 ASP cc_start: 0.8125 (p0) cc_final: 0.7838 (p0) REVERT: E 79 MET cc_start: 0.8581 (tpp) cc_final: 0.7890 (tpt) REVERT: E 92 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7320 (tp) REVERT: E 117 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8394 (mm-30) REVERT: E 133 ASP cc_start: 0.8471 (t0) cc_final: 0.7794 (t0) REVERT: E 442 GLU cc_start: 0.7745 (mp0) cc_final: 0.7464 (mp0) REVERT: E 454 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8027 (mt-10) REVERT: E 524 MET cc_start: 0.8937 (tpp) cc_final: 0.8463 (tpp) REVERT: e 92 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8305 (tp) REVERT: e 442 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: e 447 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8187 (mtm180) REVERT: e 499 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8165 (mmm) REVERT: g 38 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8342 (ttt-90) REVERT: g 69 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8203 (mm-30) REVERT: g 71 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7933 (mp10) REVERT: g 124 SER cc_start: 0.9438 (m) cc_final: 0.9144 (p) REVERT: G 20 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6173 (ttp80) REVERT: G 38 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.7775 (tmm-80) REVERT: G 45 SER cc_start: 0.9271 (OUTLIER) cc_final: 0.8864 (p) REVERT: G 49 MET cc_start: 0.8734 (tpp) cc_final: 0.8475 (mmt) REVERT: G 132 ASP cc_start: 0.8243 (m-30) cc_final: 0.8007 (m-30) REVERT: G 415 GLU cc_start: 0.8448 (mp0) cc_final: 0.8146 (mp0) REVERT: G 442 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: h 21 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7484 (tm-30) REVERT: h 61 ASP cc_start: 0.8220 (t70) cc_final: 0.7875 (t70) REVERT: h 105 LEU cc_start: 0.9416 (mt) cc_final: 0.9058 (mt) REVERT: h 387 ARG cc_start: 0.7237 (ptm-80) cc_final: 0.6910 (ptm160) REVERT: h 388 SER cc_start: 0.7930 (OUTLIER) cc_final: 0.7597 (p) REVERT: h 394 MET cc_start: 0.8137 (mmp) cc_final: 0.7885 (mmp) REVERT: h 443 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8285 (mt-10) REVERT: h 497 MET cc_start: 0.8602 (mmm) cc_final: 0.8264 (mmm) REVERT: h 508 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: H 422 ASP cc_start: 0.8725 (m-30) cc_final: 0.8280 (p0) REVERT: Q 14 MET cc_start: 0.4663 (ppp) cc_final: 0.4090 (ptp) REVERT: Q 38 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8339 (pt0) REVERT: Q 79 GLN cc_start: 0.8613 (mp10) cc_final: 0.8246 (mp10) REVERT: Q 116 GLU cc_start: 0.8036 (tp30) cc_final: 0.7497 (tp30) REVERT: Q 120 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8444 (mmt-90) REVERT: q 31 ARG cc_start: 0.8584 (mpt180) cc_final: 0.8373 (mtt90) REVERT: q 41 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8419 (tp40) REVERT: q 55 MET cc_start: 0.9069 (mtp) cc_final: 0.8843 (mtm) REVERT: q 75 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8060 (mm-30) REVERT: q 114 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8893 (mm) REVERT: q 385 MET cc_start: 0.4941 (mtt) cc_final: 0.3593 (ttt) REVERT: Z 90 ASP cc_start: 0.7734 (t0) cc_final: 0.7500 (t0) REVERT: Z 442 ASP cc_start: 0.8285 (m-30) cc_final: 0.7955 (m-30) REVERT: Z 453 GLN cc_start: 0.9247 (mt0) cc_final: 0.8959 (mt0) REVERT: Z 459 LEU cc_start: 0.9181 (tt) cc_final: 0.8913 (pp) REVERT: Z 467 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8503 (mm-40) REVERT: Z 520 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7583 (tm-30) REVERT: z 46 MET cc_start: 0.8069 (ttm) cc_final: 0.7811 (ttm) REVERT: z 63 LEU cc_start: 0.9132 (mm) cc_final: 0.8888 (mp) REVERT: z 99 ILE cc_start: 0.8978 (mt) cc_final: 0.8701 (mm) REVERT: z 520 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8073 (mm-30) outliers start: 158 outliers final: 95 residues processed: 863 average time/residue: 0.2058 time to fit residues: 285.4100 Evaluate side-chains 789 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 675 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 156 ARG Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 489 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 82 GLN Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 442 GLU Chi-restraints excluded: chain e residue 462 GLU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 444 LEU Chi-restraints excluded: chain g residue 501 VAL Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 388 SER Chi-restraints excluded: chain h residue 433 LEU Chi-restraints excluded: chain h residue 477 VAL Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain h residue 518 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 479 ILE Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 76 LEU Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 465 SER Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain Q residue 518 VAL Chi-restraints excluded: chain Q residue 519 LEU Chi-restraints excluded: chain q residue 13 GLN Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain q residue 512 THR Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 112 GLU Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 467 GLN Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 47 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 136 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 384 LEU Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 505 LEU Chi-restraints excluded: chain z residue 520 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 200 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 357 optimal weight: 4.9990 chunk 287 optimal weight: 9.9990 chunk 184 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN b 195 ASN b 391 HIS b 426 ASN b 453 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 82 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS E 520 GLN e 120 GLN e 127 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 463 ASN Z 23 ASN Z 454 ASN z 23 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.121001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.105779 restraints weight = 78759.338| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 3.30 r_work: 0.3507 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34276 Z= 0.174 Angle : 0.682 14.488 46321 Z= 0.336 Chirality : 0.043 0.286 5617 Planarity : 0.004 0.044 5931 Dihedral : 5.220 91.579 4773 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.74 % Allowed : 21.04 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.13), residues: 4407 helix: 1.60 (0.09), residues: 2905 sheet: -0.44 (0.36), residues: 199 loop : -1.40 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 433 TYR 0.020 0.002 TYR q 505 PHE 0.027 0.002 PHE q 103 TRP 0.012 0.001 TRP g 435 HIS 0.010 0.001 HIS Z 65 Details of bonding type rmsd covalent geometry : bond 0.00401 (34273) covalent geometry : angle 0.68207 (46321) hydrogen bonds : bond 0.04318 ( 2162) hydrogen bonds : angle 4.02310 ( 6366) Misc. bond : bond 0.00095 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 744 time to evaluate : 1.266 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 18 ARG cc_start: 0.8344 (mtm110) cc_final: 0.8141 (mtm110) REVERT: a 20 GLN cc_start: 0.9267 (mt0) cc_final: 0.8584 (mm-40) REVERT: a 95 ILE cc_start: 0.9419 (pt) cc_final: 0.9133 (mt) REVERT: a 99 GLU cc_start: 0.8367 (tp30) cc_final: 0.7929 (tp30) REVERT: a 106 GLU cc_start: 0.8169 (tp30) cc_final: 0.7760 (tp30) REVERT: a 110 GLN cc_start: 0.8939 (mt0) cc_final: 0.8578 (mt0) REVERT: A 105 ASP cc_start: 0.8675 (t70) cc_final: 0.8283 (t0) REVERT: A 109 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8460 (mmtp) REVERT: b 49 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7692 (t0) REVERT: b 82 LYS cc_start: 0.9213 (ttmt) cc_final: 0.8566 (tptp) REVERT: b 111 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.8389 (ptp-110) REVERT: b 120 LYS cc_start: 0.9432 (mtmt) cc_final: 0.9115 (mmtm) REVERT: b 156 ARG cc_start: 0.5335 (OUTLIER) cc_final: 0.4659 (ttp-110) REVERT: b 408 TYR cc_start: 0.8536 (m-80) cc_final: 0.8173 (m-10) REVERT: b 441 LYS cc_start: 0.8915 (mptt) cc_final: 0.8502 (mptt) REVERT: B 30 ILE cc_start: 0.7239 (mm) cc_final: 0.6807 (tt) REVERT: B 66 ASP cc_start: 0.7996 (t0) cc_final: 0.7732 (t0) REVERT: B 91 GLN cc_start: 0.8080 (tp-100) cc_final: 0.7535 (tp-100) REVERT: B 438 SER cc_start: 0.9467 (OUTLIER) cc_final: 0.9096 (p) REVERT: D 57 MET cc_start: 0.8882 (mmm) cc_final: 0.8294 (mmm) REVERT: D 459 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8443 (mm-30) REVERT: d 49 ARG cc_start: 0.8923 (ptm-80) cc_final: 0.8635 (ttp80) REVERT: d 82 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7925 (pp30) REVERT: d 483 ARG cc_start: 0.8970 (mtt90) cc_final: 0.8689 (mtt180) REVERT: E 79 MET cc_start: 0.8533 (tpp) cc_final: 0.7891 (tpt) REVERT: E 117 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8410 (mm-30) REVERT: E 524 MET cc_start: 0.8916 (tpp) cc_final: 0.8474 (tpp) REVERT: e 442 GLU cc_start: 0.7907 (tt0) cc_final: 0.7580 (tt0) REVERT: e 499 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: g 38 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8486 (ttp80) REVERT: g 69 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8197 (mm-30) REVERT: g 71 GLN cc_start: 0.8195 (mm-40) cc_final: 0.7971 (mp10) REVERT: g 124 SER cc_start: 0.9421 (m) cc_final: 0.9174 (p) REVERT: G 20 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6282 (ttp80) REVERT: G 38 ARG cc_start: 0.9246 (OUTLIER) cc_final: 0.7762 (tmm-80) REVERT: G 45 SER cc_start: 0.9173 (OUTLIER) cc_final: 0.8967 (p) REVERT: G 69 GLU cc_start: 0.7587 (tp30) cc_final: 0.7291 (tm-30) REVERT: G 415 GLU cc_start: 0.8462 (mp0) cc_final: 0.8172 (mp0) REVERT: G 442 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: G 489 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7413 (t70) REVERT: h 21 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7434 (tm-30) REVERT: h 61 ASP cc_start: 0.8243 (t70) cc_final: 0.7908 (t70) REVERT: h 105 LEU cc_start: 0.9385 (mt) cc_final: 0.8993 (mt) REVERT: h 170 GLN cc_start: 0.5625 (tm-30) cc_final: 0.5343 (tm-30) REVERT: h 387 ARG cc_start: 0.7296 (ptm-80) cc_final: 0.6983 (ptm160) REVERT: h 388 SER cc_start: 0.7862 (OUTLIER) cc_final: 0.7523 (p) REVERT: h 394 MET cc_start: 0.8048 (mmp) cc_final: 0.7775 (mmp) REVERT: h 497 MET cc_start: 0.8610 (mmm) cc_final: 0.8174 (mmm) REVERT: h 508 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: H 45 MET cc_start: 0.8016 (ttm) cc_final: 0.7406 (ttt) REVERT: H 103 GLU cc_start: 0.8293 (tp30) cc_final: 0.7830 (tp30) REVERT: H 106 LYS cc_start: 0.8859 (tttp) cc_final: 0.8429 (ttpt) REVERT: H 116 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8456 (mm) REVERT: H 422 ASP cc_start: 0.8739 (m-30) cc_final: 0.8292 (p0) REVERT: H 521 LYS cc_start: 0.8404 (ttpp) cc_final: 0.7893 (tmtt) REVERT: Q 14 MET cc_start: 0.4592 (ppp) cc_final: 0.3502 (ptp) REVERT: Q 38 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8433 (pt0) REVERT: Q 79 GLN cc_start: 0.8604 (mp10) cc_final: 0.8300 (mp10) REVERT: Q 90 SER cc_start: 0.9441 (OUTLIER) cc_final: 0.9103 (p) REVERT: Q 116 GLU cc_start: 0.7963 (tp30) cc_final: 0.7254 (tp30) REVERT: Q 120 ARG cc_start: 0.8909 (mmt90) cc_final: 0.8503 (mmt-90) REVERT: q 31 ARG cc_start: 0.8449 (mpt180) cc_final: 0.8184 (mtt90) REVERT: q 41 GLN cc_start: 0.8819 (mm-40) cc_final: 0.8365 (tp-100) REVERT: q 55 MET cc_start: 0.9052 (mtp) cc_final: 0.8806 (mtm) REVERT: q 114 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8897 (mm) REVERT: q 385 MET cc_start: 0.4650 (mtt) cc_final: 0.3317 (ttm) REVERT: Z 35 ARG cc_start: 0.8677 (ptp-170) cc_final: 0.8454 (ptp-170) REVERT: Z 76 LEU cc_start: 0.8493 (mt) cc_final: 0.8234 (mt) REVERT: Z 442 ASP cc_start: 0.8316 (m-30) cc_final: 0.7998 (m-30) REVERT: Z 453 GLN cc_start: 0.9214 (mt0) cc_final: 0.8960 (mt0) REVERT: Z 467 GLN cc_start: 0.8601 (tt0) cc_final: 0.8369 (mm-40) REVERT: Z 520 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7619 (tm-30) REVERT: z 99 ILE cc_start: 0.8844 (mt) cc_final: 0.8599 (mm) REVERT: z 520 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8033 (mm-30) outliers start: 136 outliers final: 81 residues processed: 837 average time/residue: 0.2046 time to fit residues: 273.0634 Evaluate side-chains 790 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 692 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 405 SER Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain b residue 42 THR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 156 ARG Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 480 LEU Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 82 GLN Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 535 VAL Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 75 ILE Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 499 MET Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 444 LEU Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 45 SER Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain G residue 489 ASP Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 388 SER Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain h residue 521 LYS Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 492 VAL Chi-restraints excluded: chain Q residue 39 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 465 SER Chi-restraints excluded: chain Q residue 480 LEU Chi-restraints excluded: chain q residue 13 GLN Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain q residue 524 ILE Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 37 ASN Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 93 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 112 GLU Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 198 HIS Chi-restraints excluded: chain z residue 384 LEU Chi-restraints excluded: chain z residue 408 VAL Chi-restraints excluded: chain z residue 520 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 148 optimal weight: 0.9980 chunk 251 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 290 optimal weight: 10.0000 chunk 425 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 308 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 339 optimal weight: 0.0970 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS B 453 ASN D 468 ASN d 82 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 HIS ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 448 GLN Z 23 ASN Z 454 ASN z 386 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.123543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.108483 restraints weight = 77937.067| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.22 r_work: 0.3556 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.7742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34276 Z= 0.125 Angle : 0.653 14.200 46321 Z= 0.320 Chirality : 0.041 0.206 5617 Planarity : 0.004 0.043 5931 Dihedral : 4.973 96.673 4773 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.83 % Allowed : 21.95 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.29 (0.13), residues: 4407 helix: 1.85 (0.10), residues: 2896 sheet: -0.18 (0.36), residues: 187 loop : -1.26 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 433 TYR 0.021 0.001 TYR H 423 PHE 0.018 0.001 PHE q 103 TRP 0.008 0.001 TRP g 435 HIS 0.012 0.001 HIS b 391 Details of bonding type rmsd covalent geometry : bond 0.00282 (34273) covalent geometry : angle 0.65310 (46321) hydrogen bonds : bond 0.03728 ( 2162) hydrogen bonds : angle 3.84254 ( 6366) Misc. bond : bond 0.00066 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 774 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 20 GLN cc_start: 0.9223 (mt0) cc_final: 0.8565 (mm-40) REVERT: a 95 ILE cc_start: 0.9363 (pt) cc_final: 0.9052 (mt) REVERT: a 99 GLU cc_start: 0.8332 (tp30) cc_final: 0.7992 (tp30) REVERT: a 106 GLU cc_start: 0.8134 (tp30) cc_final: 0.7793 (tp30) REVERT: A 105 ASP cc_start: 0.8656 (t70) cc_final: 0.8455 (t0) REVERT: A 109 LYS cc_start: 0.8896 (mmtp) cc_final: 0.8639 (mmtp) REVERT: A 110 GLN cc_start: 0.8290 (mp-120) cc_final: 0.8057 (mp10) REVERT: b 49 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7845 (t0) REVERT: b 82 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8541 (tptp) REVERT: b 97 ASP cc_start: 0.5164 (t0) cc_final: 0.4056 (m-30) REVERT: b 111 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8306 (ptp-110) REVERT: b 120 LYS cc_start: 0.9416 (mtmt) cc_final: 0.9117 (mmtm) REVERT: b 408 TYR cc_start: 0.8504 (m-80) cc_final: 0.8145 (m-10) REVERT: b 441 LYS cc_start: 0.8899 (mptt) cc_final: 0.8453 (mptt) REVERT: b 460 ASP cc_start: 0.8649 (t0) cc_final: 0.8321 (t0) REVERT: B 73 ASN cc_start: 0.8527 (p0) cc_final: 0.8293 (p0) REVERT: B 91 GLN cc_start: 0.8114 (tp-100) cc_final: 0.7351 (tp40) REVERT: B 438 SER cc_start: 0.9463 (OUTLIER) cc_final: 0.9098 (p) REVERT: D 57 MET cc_start: 0.8756 (mmm) cc_final: 0.8243 (mmm) REVERT: D 143 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.6917 (tppp) REVERT: D 459 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8436 (mm-30) REVERT: d 49 ARG cc_start: 0.8832 (ptm-80) cc_final: 0.8589 (ttp80) REVERT: d 82 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: d 481 ARG cc_start: 0.8943 (ttp-170) cc_final: 0.8572 (ttp-170) REVERT: E 79 MET cc_start: 0.8417 (tpp) cc_final: 0.7927 (tpt) REVERT: E 117 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8408 (mm-30) REVERT: E 124 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7389 (mtp180) REVERT: E 444 TYR cc_start: 0.8262 (m-10) cc_final: 0.7330 (m-80) REVERT: E 447 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7333 (mtt180) REVERT: E 506 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8163 (mm-30) REVERT: E 524 MET cc_start: 0.9011 (tpp) cc_final: 0.8478 (tpp) REVERT: e 442 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7600 (tt0) REVERT: e 458 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8511 (tpp) REVERT: e 463 ASN cc_start: 0.8833 (m-40) cc_final: 0.8542 (m110) REVERT: e 521 MET cc_start: 0.8565 (tpt) cc_final: 0.8255 (tpp) REVERT: g 38 ARG cc_start: 0.8897 (mmm-85) cc_final: 0.8431 (ttp80) REVERT: g 69 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8020 (mm-30) REVERT: g 503 LEU cc_start: 0.9037 (mt) cc_final: 0.8825 (mt) REVERT: G 38 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.7471 (tmm-80) REVERT: G 49 MET cc_start: 0.8679 (mmt) cc_final: 0.8312 (mmt) REVERT: G 59 MET cc_start: 0.8327 (tpp) cc_final: 0.7765 (mmm) REVERT: G 69 GLU cc_start: 0.7604 (tp30) cc_final: 0.7294 (tm-30) REVERT: G 415 GLU cc_start: 0.8446 (mp0) cc_final: 0.8148 (mp0) REVERT: h 21 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7362 (tm-30) REVERT: h 61 ASP cc_start: 0.8129 (t70) cc_final: 0.7853 (t70) REVERT: h 105 LEU cc_start: 0.9345 (mt) cc_final: 0.8946 (mt) REVERT: h 170 GLN cc_start: 0.5959 (tm-30) cc_final: 0.5656 (tm-30) REVERT: h 387 ARG cc_start: 0.7235 (ptm-80) cc_final: 0.6943 (ptm160) REVERT: h 388 SER cc_start: 0.7819 (OUTLIER) cc_final: 0.7536 (p) REVERT: h 394 MET cc_start: 0.7961 (mmp) cc_final: 0.7679 (mmp) REVERT: h 497 MET cc_start: 0.8539 (mmm) cc_final: 0.8307 (mmm) REVERT: h 508 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: H 116 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8528 (mm) REVERT: H 415 GLU cc_start: 0.9055 (tp30) cc_final: 0.8782 (tp30) REVERT: H 455 PHE cc_start: 0.8375 (m-80) cc_final: 0.8124 (m-80) REVERT: H 484 ILE cc_start: 0.8811 (pt) cc_final: 0.8453 (mt) REVERT: H 521 LYS cc_start: 0.8387 (ttpp) cc_final: 0.7972 (tmtt) REVERT: Q 14 MET cc_start: 0.4426 (ppp) cc_final: 0.3341 (ptp) REVERT: Q 38 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8436 (pt0) REVERT: Q 79 GLN cc_start: 0.8537 (mp10) cc_final: 0.8239 (mp10) REVERT: Q 90 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.9102 (p) REVERT: Q 116 GLU cc_start: 0.7861 (tp30) cc_final: 0.7176 (tp30) REVERT: Q 120 ARG cc_start: 0.8838 (mmt90) cc_final: 0.8457 (mmt-90) REVERT: q 31 ARG cc_start: 0.8467 (mpt180) cc_final: 0.8185 (mtt90) REVERT: q 34 GLN cc_start: 0.8369 (tp40) cc_final: 0.7927 (mm110) REVERT: q 41 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8303 (tp-100) REVERT: q 74 ARG cc_start: 0.8731 (ttp80) cc_final: 0.8330 (tmm-80) REVERT: q 114 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8838 (mm) REVERT: q 133 GLU cc_start: 0.8444 (mp0) cc_final: 0.8218 (mp0) REVERT: q 385 MET cc_start: 0.4317 (mtt) cc_final: 0.3396 (ttt) REVERT: Z 35 ARG cc_start: 0.8543 (ptp-170) cc_final: 0.8336 (ptp-170) REVERT: Z 442 ASP cc_start: 0.8242 (m-30) cc_final: 0.7905 (m-30) REVERT: Z 462 THR cc_start: 0.9229 (m) cc_final: 0.8932 (t) REVERT: Z 520 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7631 (tm-30) REVERT: z 23 ASN cc_start: 0.8501 (m110) cc_final: 0.7994 (m110) REVERT: z 99 ILE cc_start: 0.8717 (mt) cc_final: 0.8442 (mm) REVERT: z 380 ASN cc_start: 0.8212 (m-40) cc_final: 0.7953 (m-40) outliers start: 103 outliers final: 61 residues processed: 841 average time/residue: 0.2072 time to fit residues: 281.0106 Evaluate side-chains 773 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 699 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 82 GLN Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 519 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 442 GLU Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 444 LEU Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 85 SER Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 388 SER Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 121 ILE Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 465 SER Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 386 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 203 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 429 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 175 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 241 optimal weight: 0.0370 chunk 341 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS B 519 ASN D 468 ASN D 472 ASN d 82 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN E 493 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 471 HIS Z 23 ASN ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.124977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109628 restraints weight = 78058.889| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 3.34 r_work: 0.3569 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34276 Z= 0.124 Angle : 0.666 17.940 46321 Z= 0.325 Chirality : 0.041 0.218 5617 Planarity : 0.004 0.052 5931 Dihedral : 4.820 98.239 4773 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.39 % Allowed : 22.36 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.39 (0.13), residues: 4407 helix: 1.90 (0.09), residues: 2892 sheet: -0.25 (0.37), residues: 175 loop : -1.12 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 443 TYR 0.029 0.001 TYR Q 468 PHE 0.013 0.001 PHE Z 457 TRP 0.008 0.001 TRP g 435 HIS 0.013 0.001 HIS b 391 Details of bonding type rmsd covalent geometry : bond 0.00280 (34273) covalent geometry : angle 0.66573 (46321) hydrogen bonds : bond 0.03604 ( 2162) hydrogen bonds : angle 3.79926 ( 6366) Misc. bond : bond 0.00068 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 755 time to evaluate : 1.108 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 20 GLN cc_start: 0.9207 (mt0) cc_final: 0.8542 (mm-40) REVERT: a 77 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7724 (mp0) REVERT: a 95 ILE cc_start: 0.9345 (pt) cc_final: 0.9056 (mt) REVERT: a 99 GLU cc_start: 0.8345 (tp30) cc_final: 0.8006 (tp30) REVERT: a 106 GLU cc_start: 0.8175 (tp30) cc_final: 0.7811 (tp30) REVERT: a 433 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8103 (mtm-85) REVERT: a 434 GLU cc_start: 0.8563 (mp0) cc_final: 0.8246 (mp0) REVERT: A 109 LYS cc_start: 0.8952 (mmtp) cc_final: 0.8668 (mmtp) REVERT: A 110 GLN cc_start: 0.8202 (mp-120) cc_final: 0.7945 (mp10) REVERT: A 443 ARG cc_start: 0.8783 (ttm-80) cc_final: 0.8492 (ttp-110) REVERT: b 49 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7803 (t0) REVERT: b 82 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8554 (tptp) REVERT: b 97 ASP cc_start: 0.4963 (t0) cc_final: 0.4028 (m-30) REVERT: b 111 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8237 (ptp-110) REVERT: b 120 LYS cc_start: 0.9421 (mtmt) cc_final: 0.9120 (mmtm) REVERT: b 408 TYR cc_start: 0.8431 (m-80) cc_final: 0.8116 (m-10) REVERT: b 437 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7711 (tm-30) REVERT: b 441 LYS cc_start: 0.8904 (mptt) cc_final: 0.8482 (mptt) REVERT: b 460 ASP cc_start: 0.8625 (t0) cc_final: 0.8332 (t0) REVERT: B 66 ASP cc_start: 0.8013 (t0) cc_final: 0.7781 (t70) REVERT: B 73 ASN cc_start: 0.8378 (p0) cc_final: 0.8173 (p0) REVERT: B 89 ARG cc_start: 0.8010 (tpp80) cc_final: 0.7702 (tpp80) REVERT: B 91 GLN cc_start: 0.8084 (tp-100) cc_final: 0.7432 (tp40) REVERT: B 120 LYS cc_start: 0.9373 (mmmt) cc_final: 0.9119 (mmmt) REVERT: B 438 SER cc_start: 0.9404 (m) cc_final: 0.9107 (p) REVERT: D 57 MET cc_start: 0.8763 (mmm) cc_final: 0.8242 (mmm) REVERT: D 143 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6719 (tppp) REVERT: D 459 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8421 (mm-30) REVERT: d 49 ARG cc_start: 0.8816 (ptm-80) cc_final: 0.8515 (ttp80) REVERT: d 82 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: d 90 MET cc_start: 0.8355 (ptp) cc_final: 0.8069 (mtm) REVERT: E 79 MET cc_start: 0.8316 (tpp) cc_final: 0.7742 (tpt) REVERT: E 117 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8405 (mm-30) REVERT: E 124 ARG cc_start: 0.8224 (mtp85) cc_final: 0.7563 (mtp85) REVERT: E 442 GLU cc_start: 0.7508 (mp0) cc_final: 0.7178 (mp0) REVERT: E 444 TYR cc_start: 0.8358 (m-10) cc_final: 0.8088 (m-80) REVERT: E 447 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7298 (mtt180) REVERT: E 524 MET cc_start: 0.9046 (tpp) cc_final: 0.8532 (tpp) REVERT: e 398 ARG cc_start: 0.7808 (tpp-160) cc_final: 0.7572 (tpp-160) REVERT: e 442 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: e 458 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8537 (tpp) REVERT: g 38 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8425 (ttp80) REVERT: g 58 VAL cc_start: 0.8473 (t) cc_final: 0.8187 (p) REVERT: g 69 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7972 (mm-30) REVERT: g 511 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8280 (tm-30) REVERT: G 38 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.7486 (tmm-80) REVERT: G 69 GLU cc_start: 0.7472 (tp30) cc_final: 0.7155 (tm-30) REVERT: G 87 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7746 (tm-30) REVERT: G 93 ASP cc_start: 0.8034 (t0) cc_final: 0.7780 (t0) REVERT: G 415 GLU cc_start: 0.8413 (mp0) cc_final: 0.8111 (mp0) REVERT: G 461 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8310 (mtt90) REVERT: G 490 MET cc_start: 0.7885 (mmm) cc_final: 0.6894 (mmm) REVERT: h 21 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7377 (tm-30) REVERT: h 61 ASP cc_start: 0.8255 (t70) cc_final: 0.7934 (t70) REVERT: h 105 LEU cc_start: 0.9318 (mt) cc_final: 0.8926 (mt) REVERT: h 170 GLN cc_start: 0.5866 (tm-30) cc_final: 0.5594 (tm-30) REVERT: h 387 ARG cc_start: 0.7229 (ptm-80) cc_final: 0.6942 (ptm160) REVERT: h 388 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7341 (p) REVERT: h 394 MET cc_start: 0.7961 (mmp) cc_final: 0.7673 (mmp) REVERT: h 508 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: H 116 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8616 (mm) REVERT: H 415 GLU cc_start: 0.8875 (tp30) cc_final: 0.8563 (tp30) REVERT: H 518 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8243 (tm-30) REVERT: H 521 LYS cc_start: 0.8376 (ttpp) cc_final: 0.7988 (tmtt) REVERT: Q 14 MET cc_start: 0.4387 (ppp) cc_final: 0.3361 (ptp) REVERT: Q 38 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8438 (pt0) REVERT: Q 79 GLN cc_start: 0.8628 (mp10) cc_final: 0.8258 (mp10) REVERT: Q 116 GLU cc_start: 0.7874 (tp30) cc_final: 0.7180 (tp30) REVERT: Q 120 ARG cc_start: 0.8862 (mmt90) cc_final: 0.8495 (mmt-90) REVERT: q 31 ARG cc_start: 0.8505 (mpt180) cc_final: 0.8243 (mtt90) REVERT: q 34 GLN cc_start: 0.8343 (tp40) cc_final: 0.7860 (mm110) REVERT: q 41 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8196 (tp-100) REVERT: q 74 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8345 (tmm-80) REVERT: q 133 GLU cc_start: 0.8423 (mp0) cc_final: 0.8164 (mp0) REVERT: q 385 MET cc_start: 0.4458 (mtt) cc_final: 0.3584 (ttt) REVERT: Z 442 ASP cc_start: 0.8303 (m-30) cc_final: 0.7958 (m-30) REVERT: Z 453 GLN cc_start: 0.9142 (mt0) cc_final: 0.8851 (mt0) REVERT: Z 520 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7673 (tm-30) REVERT: z 44 MET cc_start: 0.8949 (mtt) cc_final: 0.8723 (mmt) REVERT: z 99 ILE cc_start: 0.8702 (mt) cc_final: 0.8413 (mm) outliers start: 87 outliers final: 62 residues processed: 812 average time/residue: 0.2022 time to fit residues: 263.1956 Evaluate side-chains 770 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 697 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 499 LYS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 391 HIS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 478 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 82 GLN Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain d residue 504 LEU Chi-restraints excluded: chain d residue 519 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 404 LEU Chi-restraints excluded: chain e residue 442 GLU Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 444 LEU Chi-restraints excluded: chain g residue 455 CYS Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 461 ARG Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 388 SER Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 465 SER Chi-restraints excluded: chain q residue 118 LEU Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 73 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 112 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 389 optimal weight: 7.9990 chunk 203 optimal weight: 0.0770 chunk 15 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 377 optimal weight: 0.1980 chunk 54 optimal weight: 0.0970 chunk 257 optimal weight: 5.9990 chunk 259 optimal weight: 0.0370 chunk 192 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 overall best weight: 0.2614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN b 391 HIS B 91 GLN D 468 ASN d 82 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN E 467 ASN E 493 HIS e 145 HIS h 201 GLN ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 380 ASN z 386 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.127418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.113064 restraints weight = 74908.739| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.26 r_work: 0.3616 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34276 Z= 0.124 Angle : 0.689 24.526 46321 Z= 0.332 Chirality : 0.041 0.207 5617 Planarity : 0.004 0.084 5931 Dihedral : 4.752 99.444 4773 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.14 % Allowed : 23.57 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.52 (0.13), residues: 4407 helix: 1.99 (0.10), residues: 2883 sheet: -0.09 (0.37), residues: 175 loop : -1.03 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG a 18 TYR 0.024 0.001 TYR H 423 PHE 0.015 0.001 PHE Q 103 TRP 0.006 0.000 TRP g 435 HIS 0.020 0.001 HIS b 391 Details of bonding type rmsd covalent geometry : bond 0.00276 (34273) covalent geometry : angle 0.68908 (46321) hydrogen bonds : bond 0.03436 ( 2162) hydrogen bonds : angle 3.76676 ( 6366) Misc. bond : bond 0.00065 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8814 Ramachandran restraints generated. 4407 Oldfield, 0 Emsley, 4407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 776 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 ILE cc_start: 0.9354 (pt) cc_final: 0.9071 (mt) REVERT: a 99 GLU cc_start: 0.8331 (tp30) cc_final: 0.7959 (tp30) REVERT: a 106 GLU cc_start: 0.8143 (tp30) cc_final: 0.7767 (tp30) REVERT: a 433 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.8078 (mtm-85) REVERT: a 434 GLU cc_start: 0.8619 (mp0) cc_final: 0.8205 (mp0) REVERT: b 49 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7681 (t0) REVERT: b 82 LYS cc_start: 0.9157 (ttmt) cc_final: 0.8531 (tptp) REVERT: b 97 ASP cc_start: 0.5494 (t0) cc_final: 0.4576 (m-30) REVERT: b 120 LYS cc_start: 0.9413 (mtmt) cc_final: 0.9111 (mmtm) REVERT: b 408 TYR cc_start: 0.8385 (m-80) cc_final: 0.8100 (m-10) REVERT: b 437 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7650 (tm-30) REVERT: b 441 LYS cc_start: 0.8854 (mptt) cc_final: 0.8468 (mptt) REVERT: b 460 ASP cc_start: 0.8274 (t0) cc_final: 0.7923 (t0) REVERT: B 66 ASP cc_start: 0.7987 (t0) cc_final: 0.7691 (t70) REVERT: B 73 ASN cc_start: 0.8281 (p0) cc_final: 0.8045 (p0) REVERT: B 89 ARG cc_start: 0.7990 (tpp80) cc_final: 0.7643 (tpp80) REVERT: B 91 GLN cc_start: 0.8030 (tp40) cc_final: 0.7415 (tp40) REVERT: B 438 SER cc_start: 0.9371 (m) cc_final: 0.9102 (p) REVERT: D 57 MET cc_start: 0.8787 (mmm) cc_final: 0.8504 (mmt) REVERT: D 143 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6478 (tppp) REVERT: d 49 ARG cc_start: 0.8736 (ptm-80) cc_final: 0.8479 (ttp80) REVERT: d 63 ASP cc_start: 0.6290 (p0) cc_final: 0.6052 (p0) REVERT: d 82 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7130 (tm-30) REVERT: d 90 MET cc_start: 0.8401 (ptp) cc_final: 0.8140 (mtm) REVERT: E 79 MET cc_start: 0.8255 (tpp) cc_final: 0.7590 (tpt) REVERT: E 117 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8442 (mm-30) REVERT: E 124 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7437 (mtp85) REVERT: E 144 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8500 (pp20) REVERT: E 444 TYR cc_start: 0.8346 (m-10) cc_final: 0.7963 (m-80) REVERT: E 454 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8098 (mt-10) REVERT: E 470 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7711 (tm-30) REVERT: E 524 MET cc_start: 0.9096 (tpp) cc_final: 0.8646 (tpp) REVERT: E 529 ASP cc_start: 0.8668 (p0) cc_final: 0.8465 (p0) REVERT: e 398 ARG cc_start: 0.7849 (tpp-160) cc_final: 0.7621 (tpp-160) REVERT: e 458 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8500 (tpp) REVERT: g 38 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8471 (ttp80) REVERT: g 58 VAL cc_start: 0.8393 (t) cc_final: 0.8125 (p) REVERT: g 69 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7898 (mm-30) REVERT: g 87 GLN cc_start: 0.8910 (tp40) cc_final: 0.8667 (tp40) REVERT: g 511 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8312 (tm-30) REVERT: G 38 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.7348 (tmm-80) REVERT: G 49 MET cc_start: 0.8850 (mmt) cc_final: 0.8587 (mmt) REVERT: G 54 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7351 (mpp) REVERT: G 87 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7685 (tm-30) REVERT: G 93 ASP cc_start: 0.8062 (t0) cc_final: 0.7793 (t0) REVERT: G 132 ASP cc_start: 0.8117 (m-30) cc_final: 0.7695 (m-30) REVERT: G 415 GLU cc_start: 0.8368 (mp0) cc_final: 0.8102 (mp0) REVERT: G 461 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8317 (mtt90) REVERT: G 489 ASP cc_start: 0.7982 (m-30) cc_final: 0.7537 (t70) REVERT: G 490 MET cc_start: 0.7886 (mmm) cc_final: 0.7234 (mmm) REVERT: h 21 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7306 (tm-30) REVERT: h 61 ASP cc_start: 0.8410 (t70) cc_final: 0.8040 (t70) REVERT: h 105 LEU cc_start: 0.9318 (mt) cc_final: 0.8927 (mt) REVERT: h 170 GLN cc_start: 0.5745 (tm-30) cc_final: 0.5459 (tm-30) REVERT: h 201 GLN cc_start: 0.5938 (OUTLIER) cc_final: 0.5682 (mt0) REVERT: h 387 ARG cc_start: 0.7097 (ptm-80) cc_final: 0.6803 (ptm160) REVERT: h 388 SER cc_start: 0.7616 (OUTLIER) cc_final: 0.7300 (p) REVERT: h 394 MET cc_start: 0.8012 (mmp) cc_final: 0.7735 (mmp) REVERT: h 508 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: H 116 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (mm) REVERT: H 415 GLU cc_start: 0.8914 (tp30) cc_final: 0.8593 (tp30) REVERT: H 440 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8774 (tptt) REVERT: H 518 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8083 (tm-30) REVERT: H 521 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8043 (tmtt) REVERT: Q 14 MET cc_start: 0.4164 (ppp) cc_final: 0.3373 (ptt) REVERT: Q 38 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8427 (pt0) REVERT: Q 79 GLN cc_start: 0.8575 (mp10) cc_final: 0.8229 (mp10) REVERT: Q 116 GLU cc_start: 0.7810 (tp30) cc_final: 0.6670 (tp30) REVERT: Q 120 ARG cc_start: 0.8803 (mmt90) cc_final: 0.8010 (mmt180) REVERT: Q 468 TYR cc_start: 0.9115 (m-80) cc_final: 0.8862 (m-10) REVERT: q 31 ARG cc_start: 0.8466 (mpt180) cc_final: 0.8124 (mpt180) REVERT: q 34 GLN cc_start: 0.8315 (tp40) cc_final: 0.7745 (mm-40) REVERT: q 41 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8175 (tp-100) REVERT: q 55 MET cc_start: 0.8727 (mtp) cc_final: 0.8502 (mtm) REVERT: q 74 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8295 (tmm-80) REVERT: q 133 GLU cc_start: 0.8450 (mp0) cc_final: 0.8141 (mp0) REVERT: q 385 MET cc_start: 0.4713 (mtt) cc_final: 0.3707 (ttm) REVERT: Z 76 LEU cc_start: 0.8519 (mt) cc_final: 0.8138 (mt) REVERT: Z 442 ASP cc_start: 0.8349 (m-30) cc_final: 0.7998 (m-30) REVERT: Z 520 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7891 (tm-30) REVERT: z 23 ASN cc_start: 0.8592 (m110) cc_final: 0.8243 (m110) REVERT: z 99 ILE cc_start: 0.8637 (mt) cc_final: 0.8344 (mt) outliers start: 78 outliers final: 49 residues processed: 821 average time/residue: 0.2041 time to fit residues: 269.5795 Evaluate side-chains 785 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 725 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 505 GLU Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 80 GLN Chi-restraints excluded: chain D residue 143 LYS Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 82 GLN Chi-restraints excluded: chain d residue 84 LEU Chi-restraints excluded: chain d residue 519 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 110 LEU Chi-restraints excluded: chain e residue 155 VAL Chi-restraints excluded: chain e residue 458 MET Chi-restraints excluded: chain g residue 36 ILE Chi-restraints excluded: chain g residue 444 LEU Chi-restraints excluded: chain g residue 455 CYS Chi-restraints excluded: chain g residue 516 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 54 MET Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 461 ARG Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain h residue 183 VAL Chi-restraints excluded: chain h residue 201 GLN Chi-restraints excluded: chain h residue 373 ILE Chi-restraints excluded: chain h residue 388 SER Chi-restraints excluded: chain h residue 508 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain Q residue 56 VAL Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain Q residue 90 SER Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 124 SER Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 429 THR Chi-restraints excluded: chain Q residue 516 VAL Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 65 HIS Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 107 ASP Chi-restraints excluded: chain z residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 132 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 280 optimal weight: 0.7980 chunk 432 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 381 optimal weight: 0.0980 chunk 51 optimal weight: 0.4980 chunk 126 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 391 HIS D 468 ASN d 82 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** g 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN Z 453 GLN z 380 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.126445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.111280 restraints weight = 78081.710| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.32 r_work: 0.3588 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.8019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34276 Z= 0.132 Angle : 0.691 17.798 46321 Z= 0.336 Chirality : 0.042 0.208 5617 Planarity : 0.004 0.082 5931 Dihedral : 4.751 98.927 4773 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.98 % Allowed : 23.93 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 1.55 (0.13), residues: 4407 helix: 2.02 (0.10), residues: 2881 sheet: -0.19 (0.36), residues: 183 loop : -1.03 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG a 18 TYR 0.025 0.001 TYR H 423 PHE 0.015 0.001 PHE Q 103 TRP 0.007 0.001 TRP g 435 HIS 0.011 0.001 HIS e 145 Details of bonding type rmsd covalent geometry : bond 0.00307 (34273) covalent geometry : angle 0.69124 (46321) hydrogen bonds : bond 0.03581 ( 2162) hydrogen bonds : angle 3.78485 ( 6366) Misc. bond : bond 0.00069 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8635.40 seconds wall clock time: 148 minutes 35.93 seconds (8915.93 seconds total)