Starting phenix.real_space_refine on Sun Jun 29 00:45:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hki_34852/06_2025/8hki_34852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hki_34852/06_2025/8hki_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_34852/06_2025/8hki_34852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hki_34852/06_2025/8hki_34852.map" model { file = "/net/cci-nas-00/data/ceres_data/8hki_34852/06_2025/8hki_34852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hki_34852/06_2025/8hki_34852.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 24.61, per 1000 atoms: 0.73 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: 7.75 Conformation dependent library (CDL) restraints added in 4.7 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: 3.78 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: 14.04 Time building geometry restraints manager: 9.39 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 526 or resid 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.170 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 80.090 Find NCS groups from input model: 1.620 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.000 TRP g 478 HIS 0.002 0.000 HIS q 59 PHE 0.014 0.001 PHE G 112 TYR 0.006 0.001 TYR g 437 ARG 0.004 0.000 ARG e 398 Details of bonding type rmsd hydrogen bonds : bond 0.26836 ( 2162) hydrogen bonds : angle 8.12817 ( 6366) covalent geometry : bond 0.00280 (34273) covalent geometry : angle 0.53130 (46321) 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 : 3.921 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: 0.5891 time to fit residues: 1498.1938 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 : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 5.9990 chunk 334 optimal weight: 0.9990 chunk 185 optimal weight: 0.0170 chunk 114 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 345 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 210 optimal weight: 0.9990 chunk 257 optimal weight: 8.9990 chunk 400 optimal weight: 2.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- 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 475 GLN ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 HIS b 174 HIS b 175 HIS b 195 ASN b 464 GLN ** B 73 ASN ** 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** e 443 GLN 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 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 382 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.136112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.121136 restraints weight = 73512.844| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.40 r_work: 0.3729 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 34276 Z= 0.172 Angle : 0.664 9.853 46321 Z= 0.338 Chirality : 0.043 0.228 5617 Planarity : 0.004 0.057 5931 Dihedral : 5.056 107.430 4773 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.30 % Allowed : 14.73 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.12), residues: 4407 helix: 0.38 (0.09), residues: 2902 sheet: -1.19 (0.35), residues: 192 loop : -1.51 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP z 495 HIS 0.007 0.001 HIS H 468 PHE 0.024 0.002 PHE a 516 TYR 0.020 0.002 TYR h 419 ARG 0.008 0.001 ARG H 53 Details of bonding type rmsd hydrogen bonds : bond 0.05004 ( 2162) hydrogen bonds : angle 4.44718 ( 6366) covalent geometry : bond 0.00394 (34273) covalent geometry : angle 0.66431 (46321) Misc. bond : bond 0.00085 ( 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 1114 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 994 time to evaluate : 3.757 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: a 108 VAL cc_start: 0.8890 (t) cc_final: 0.8635 (m) REVERT: a 424 GLU cc_start: 0.8766 (tt0) cc_final: 0.8470 (tt0) REVERT: a 527 ILE cc_start: 0.9013 (mm) cc_final: 0.8649 (mt) REVERT: a 528 ASP cc_start: 0.8250 (p0) cc_final: 0.8007 (p0) REVERT: A 51 ASP cc_start: 0.6873 (m-30) cc_final: 0.6544 (m-30) REVERT: A 528 ASP cc_start: 0.8695 (p0) cc_final: 0.8476 (p0) REVERT: b 78 ASN cc_start: 0.8119 (t0) cc_final: 0.7905 (t0) REVERT: b 82 LYS cc_start: 0.9259 (ttmm) cc_final: 0.8855 (mtmm) REVERT: b 97 ASP cc_start: 0.6476 (t0) cc_final: 0.5307 (m-30) REVERT: b 120 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8667 (mmtm) REVERT: b 414 GLU cc_start: 0.8673 (mp0) cc_final: 0.8457 (mp0) REVERT: b 452 ASP cc_start: 0.8579 (m-30) cc_final: 0.8041 (m-30) REVERT: b 458 SER cc_start: 0.8492 (p) cc_final: 0.7791 (t) REVERT: B 77 ASP cc_start: 0.7307 (p0) cc_final: 0.6055 (m-30) REVERT: B 91 GLN cc_start: 0.7292 (tp-100) cc_final: 0.6891 (tp40) REVERT: B 120 LYS cc_start: 0.8967 (tttt) cc_final: 0.8745 (mptt) REVERT: B 417 MET cc_start: 0.8014 (mtt) cc_final: 0.7760 (mpp) REVERT: B 448 THR cc_start: 0.9030 (m) cc_final: 0.8206 (p) REVERT: B 452 ASP cc_start: 0.8099 (m-30) cc_final: 0.7423 (m-30) REVERT: B 457 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7782 (p0) REVERT: D 49 ARG cc_start: 0.8558 (ptm-80) cc_final: 0.8138 (ptm160) REVERT: D 57 MET cc_start: 0.8911 (mmm) cc_final: 0.8316 (mmm) REVERT: D 122 LYS cc_start: 0.9182 (tptm) cc_final: 0.8921 (tptp) REVERT: D 472 ASN cc_start: 0.8345 (t0) cc_final: 0.8048 (t0) REVERT: d 46 ASP cc_start: 0.8653 (m-30) cc_final: 0.8445 (m-30) REVERT: d 446 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7765 (mmm) REVERT: d 454 PHE cc_start: 0.9396 (t80) cc_final: 0.9193 (t80) REVERT: d 520 THR cc_start: 0.9142 (m) cc_final: 0.8892 (p) REVERT: E 79 MET cc_start: 0.8309 (tpp) cc_final: 0.7928 (tpt) REVERT: E 117 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8143 (mm-30) REVERT: E 120 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: e 116 GLU cc_start: 0.8655 (tt0) cc_final: 0.8354 (tp30) REVERT: e 120 GLN cc_start: 0.8216 (mp10) cc_final: 0.7995 (mp10) REVERT: e 458 MET cc_start: 0.8903 (ttm) cc_final: 0.8485 (ttm) REVERT: e 531 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8955 (mm) REVERT: g 69 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7899 (mm-30) REVERT: g 132 ASP cc_start: 0.8085 (m-30) cc_final: 0.7785 (m-30) REVERT: G 35 ASP cc_start: 0.8244 (m-30) cc_final: 0.8023 (m-30) REVERT: G 47 MET cc_start: 0.8723 (mmm) cc_final: 0.8193 (mmm) REVERT: G 69 GLU cc_start: 0.7073 (tp30) cc_final: 0.6868 (tp30) REVERT: G 87 GLN cc_start: 0.8429 (tm-30) cc_final: 0.8080 (tm-30) REVERT: G 115 GLN cc_start: 0.8106 (mp10) cc_final: 0.7861 (mp10) REVERT: G 145 ASP cc_start: 0.7683 (t0) cc_final: 0.6998 (m-30) REVERT: G 511 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7667 (tp30) REVERT: G 515 LEU cc_start: 0.8662 (tt) cc_final: 0.8370 (mt) REVERT: h 21 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7175 (mm110) REVERT: h 49 ILE cc_start: 0.9022 (mt) cc_final: 0.8606 (tt) REVERT: h 57 THR cc_start: 0.9173 (m) cc_final: 0.8925 (p) REVERT: h 61 ASP cc_start: 0.7724 (t70) cc_final: 0.7414 (t70) REVERT: h 105 LEU cc_start: 0.9287 (mt) cc_final: 0.9009 (mt) REVERT: h 443 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8140 (mt-10) REVERT: h 517 ASP cc_start: 0.7529 (t0) cc_final: 0.7025 (t0) REVERT: H 87 ASP cc_start: 0.7081 (t0) cc_final: 0.6844 (t0) REVERT: H 106 LYS cc_start: 0.8628 (tttp) cc_final: 0.8217 (ttpt) REVERT: H 455 PHE cc_start: 0.7874 (m-10) cc_final: 0.7645 (m-10) REVERT: H 501 ASN cc_start: 0.8014 (m-40) cc_final: 0.7759 (m-40) REVERT: H 515 SER cc_start: 0.9193 (p) cc_final: 0.8613 (p) REVERT: Q 14 MET cc_start: 0.4926 (ppp) cc_final: 0.3872 (ptt) REVERT: Q 31 ARG cc_start: 0.7747 (mmt180) cc_final: 0.7413 (mmt-90) REVERT: Q 38 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8330 (pt0) REVERT: Q 468 TYR cc_start: 0.9082 (m-10) cc_final: 0.8795 (m-10) REVERT: Q 505 TYR cc_start: 0.8277 (t80) cc_final: 0.7691 (t80) REVERT: q 31 ARG cc_start: 0.8540 (mmt180) cc_final: 0.8259 (mpt180) REVERT: q 52 MET cc_start: 0.9002 (mmm) cc_final: 0.8595 (mmm) REVERT: q 73 LEU cc_start: 0.9148 (mt) cc_final: 0.8940 (mt) REVERT: q 75 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7301 (mm-30) REVERT: q 88 MET cc_start: 0.8242 (mtp) cc_final: 0.7917 (mmm) REVERT: q 114 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8770 (mm) REVERT: q 390 ARG cc_start: 0.9140 (ptp90) cc_final: 0.8884 (ptp90) REVERT: q 428 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8188 (pp20) REVERT: q 523 GLN cc_start: 0.8488 (tt0) cc_final: 0.8266 (tp40) REVERT: Z 35 ARG cc_start: 0.8024 (ptt90) cc_final: 0.7632 (ptp-170) REVERT: Z 121 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: Z 128 GLU cc_start: 0.8106 (tp30) cc_final: 0.7893 (tp30) REVERT: Z 135 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7560 (mm-30) REVERT: z 520 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7605 (mm-30) outliers start: 120 outliers final: 57 residues processed: 1064 average time/residue: 0.5182 time to fit residues: 881.3879 Evaluate side-chains 851 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 786 time to evaluate : 4.566 ------------------------------------------------------------------------------- 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 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 413 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 446 MET Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 78 LEU Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 529 ILE 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 484 ASN 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 121 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 388 SER 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 126 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 166 THR Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 428 GLU 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 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 36 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 408 VAL 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 313 optimal weight: 5.9990 chunk 397 optimal weight: 1.9990 chunk 409 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 199 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 357 optimal weight: 0.9990 chunk 345 optimal weight: 0.9990 chunk 176 optimal weight: 9.9990 chunk 406 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 135 ASN A 472 ASN b 423 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 HIS ** 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 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 462 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 435 GLN q 140 HIS Z 61 ASN Z 115 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.133884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.119243 restraints weight = 73742.590| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.24 r_work: 0.3697 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.5360 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= 0.136 Angle : 0.607 8.526 46321 Z= 0.303 Chirality : 0.042 0.235 5617 Planarity : 0.004 0.049 5931 Dihedral : 4.820 103.005 4773 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.13 % Allowed : 17.53 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.12), residues: 4407 helix: 1.22 (0.09), residues: 2892 sheet: -0.54 (0.36), residues: 180 loop : -1.28 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP z 495 HIS 0.017 0.001 HIS z 161 PHE 0.013 0.001 PHE q 178 TYR 0.015 0.001 TYR H 475 ARG 0.006 0.001 ARG h 37 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 2162) hydrogen bonds : angle 4.05750 ( 6366) covalent geometry : bond 0.00306 (34273) covalent geometry : angle 0.60681 (46321) Misc. bond : bond 0.00106 ( 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 997 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 883 time to evaluate : 4.096 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: a 108 VAL cc_start: 0.8954 (t) cc_final: 0.8687 (m) REVERT: a 146 ASP cc_start: 0.5139 (t0) cc_final: 0.4865 (t0) REVERT: a 443 ARG cc_start: 0.8716 (mtm110) cc_final: 0.8346 (ttp-110) REVERT: a 527 ILE cc_start: 0.8995 (mm) cc_final: 0.8656 (mt) REVERT: A 51 ASP cc_start: 0.6851 (m-30) cc_final: 0.6578 (m-30) REVERT: A 106 GLU cc_start: 0.7674 (pt0) cc_final: 0.7248 (pt0) REVERT: A 109 LYS cc_start: 0.8985 (mmtp) cc_final: 0.8733 (mmtp) REVERT: A 110 GLN cc_start: 0.8517 (mp10) cc_final: 0.8146 (mp10) REVERT: A 443 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8480 (mtp-110) REVERT: A 473 GLU cc_start: 0.8162 (tp30) cc_final: 0.7913 (tp30) REVERT: b 29 PHE cc_start: 0.8095 (m-10) cc_final: 0.7842 (m-10) REVERT: b 49 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7853 (t0) REVERT: b 63 VAL cc_start: 0.9024 (t) cc_final: 0.8817 (p) REVERT: b 97 ASP cc_start: 0.6474 (t0) cc_final: 0.5443 (m-30) REVERT: b 120 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8670 (mmtm) REVERT: b 162 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7820 (tt) REVERT: b 458 SER cc_start: 0.8569 (p) cc_final: 0.8213 (t) REVERT: b 480 MET cc_start: 0.7691 (pmm) cc_final: 0.7041 (mpp) REVERT: B 91 GLN cc_start: 0.7411 (tp-100) cc_final: 0.7085 (tp40) REVERT: B 120 LYS cc_start: 0.9083 (tttt) cc_final: 0.8853 (tptt) REVERT: B 439 TYR cc_start: 0.9067 (t80) cc_final: 0.8804 (t80) REVERT: B 448 THR cc_start: 0.9270 (m) cc_final: 0.8838 (p) REVERT: D 57 MET cc_start: 0.8880 (mmm) cc_final: 0.8302 (mmm) REVERT: D 96 LYS cc_start: 0.8805 (mmmm) cc_final: 0.8471 (mtmt) REVERT: D 459 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8514 (mm-30) REVERT: d 46 ASP cc_start: 0.8735 (m-30) cc_final: 0.8501 (m-30) REVERT: E 37 MET cc_start: 0.8613 (mmp) cc_final: 0.8399 (mmp) REVERT: E 79 MET cc_start: 0.8270 (tpp) cc_final: 0.7757 (tpt) REVERT: E 117 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8198 (mm-30) REVERT: E 444 TYR cc_start: 0.8183 (m-80) cc_final: 0.7932 (m-80) REVERT: e 80 ASP cc_start: 0.7440 (p0) cc_final: 0.7017 (t0) REVERT: e 89 MET cc_start: 0.8520 (mtm) cc_final: 0.8213 (mtp) REVERT: e 116 GLU cc_start: 0.8598 (tt0) cc_final: 0.8350 (tp30) REVERT: e 120 GLN cc_start: 0.8272 (mp10) cc_final: 0.8042 (mp10) REVERT: e 391 MET cc_start: 0.7132 (mpp) cc_final: 0.6879 (ppp) REVERT: e 442 GLU cc_start: 0.7574 (tt0) cc_final: 0.7334 (tt0) REVERT: e 463 ASN cc_start: 0.8827 (m-40) cc_final: 0.8421 (m110) REVERT: e 533 LYS cc_start: 0.7709 (tptm) cc_final: 0.7346 (tptm) REVERT: g 38 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8290 (mtp85) REVERT: g 69 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7946 (mm-30) REVERT: g 124 SER cc_start: 0.9364 (m) cc_final: 0.9109 (p) REVERT: G 47 MET cc_start: 0.8905 (mmm) cc_final: 0.8020 (mmm) REVERT: G 59 MET cc_start: 0.8006 (mmm) cc_final: 0.6900 (mtm) REVERT: G 87 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8124 (tm-30) REVERT: G 145 ASP cc_start: 0.7943 (t0) cc_final: 0.7202 (m-30) REVERT: G 521 ASP cc_start: 0.7129 (t0) cc_final: 0.6927 (m-30) REVERT: h 61 ASP cc_start: 0.8016 (t70) cc_final: 0.7677 (t70) REVERT: h 105 LEU cc_start: 0.9232 (mt) cc_final: 0.8988 (mt) REVERT: h 199 LYS cc_start: 0.5634 (tptt) cc_final: 0.4893 (tptt) REVERT: h 374 LEU cc_start: 0.7512 (mt) cc_final: 0.7265 (mt) REVERT: h 443 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8355 (mt-10) REVERT: h 451 ASP cc_start: 0.8530 (m-30) cc_final: 0.7934 (m-30) REVERT: h 517 ASP cc_start: 0.7261 (t0) cc_final: 0.7046 (t0) REVERT: H 25 ASN cc_start: 0.9083 (m-40) cc_final: 0.8765 (m110) REVERT: H 106 LYS cc_start: 0.8653 (tttp) cc_final: 0.8246 (ttpt) REVERT: H 130 GLN cc_start: 0.8027 (mm110) cc_final: 0.7735 (tp-100) REVERT: H 483 ASP cc_start: 0.7740 (p0) cc_final: 0.7519 (p0) REVERT: H 497 MET cc_start: 0.7822 (ppp) cc_final: 0.7511 (ppp) REVERT: H 501 ASN cc_start: 0.8184 (m-40) cc_final: 0.7890 (m-40) REVERT: Q 14 MET cc_start: 0.4579 (ppp) cc_final: 0.3606 (ptt) REVERT: Q 38 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8325 (pt0) REVERT: Q 116 GLU cc_start: 0.7874 (tp30) cc_final: 0.7323 (tp30) REVERT: Q 117 GLU cc_start: 0.8360 (tp30) cc_final: 0.8141 (tp30) REVERT: Q 468 TYR cc_start: 0.9090 (m-10) cc_final: 0.8835 (m-10) REVERT: Q 492 MET cc_start: 0.8002 (mmm) cc_final: 0.7802 (mmm) REVERT: q 34 GLN cc_start: 0.8271 (tp40) cc_final: 0.8031 (mm-40) REVERT: q 41 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8221 (mm-40) REVERT: q 73 LEU cc_start: 0.9162 (mt) cc_final: 0.8883 (mt) REVERT: q 114 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8820 (mm) REVERT: q 385 MET cc_start: 0.4565 (mtt) cc_final: 0.3552 (ttt) REVERT: q 523 GLN cc_start: 0.8517 (tt0) cc_final: 0.8147 (tp40) REVERT: Z 35 ARG cc_start: 0.8252 (ptt90) cc_final: 0.7879 (ptm160) REVERT: Z 70 GLN cc_start: 0.6864 (mt0) cc_final: 0.6608 (mt0) REVERT: Z 121 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: Z 128 GLU cc_start: 0.8119 (tp30) cc_final: 0.7878 (tp30) REVERT: Z 453 GLN cc_start: 0.9271 (mt0) cc_final: 0.8907 (mt0) REVERT: Z 458 ASP cc_start: 0.7945 (t0) cc_final: 0.7113 (t0) REVERT: Z 487 MET cc_start: 0.8376 (tmm) cc_final: 0.8118 (ppp) REVERT: Z 514 ASN cc_start: 0.8864 (m-40) cc_final: 0.8254 (t0) REVERT: Z 520 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7869 (tm-30) REVERT: Z 523 ARG cc_start: 0.7814 (mtt90) cc_final: 0.7601 (ttm-80) REVERT: z 23 ASN cc_start: 0.8529 (m-40) cc_final: 0.8169 (m-40) REVERT: z 46 MET cc_start: 0.7881 (ttm) cc_final: 0.7525 (ttm) REVERT: z 520 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7935 (mm-30) outliers start: 114 outliers final: 68 residues processed: 953 average time/residue: 0.4651 time to fit residues: 708.1015 Evaluate side-chains 818 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 745 time to evaluate : 4.085 ------------------------------------------------------------------------------- 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 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 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 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 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 46 MET 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 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 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 512 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain H residue 427 ILE 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 513 ASN 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 130 GLU Chi-restraints excluded: chain q residue 153 ASN Chi-restraints excluded: chain q residue 166 THR 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 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 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 406 CYS Chi-restraints excluded: chain z residue 499 CYS 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 223 optimal weight: 8.9990 chunk 264 optimal weight: 0.6980 chunk 282 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 192 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 425 optimal weight: 0.0470 chunk 158 optimal weight: 1.9990 chunk 295 optimal weight: 0.8980 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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** b 195 ASN D 502 ASN d 62 GLN ** d 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 120 GLN G 526 HIS ** 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 21 GLN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 GLN q 13 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.133657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.118908 restraints weight = 73547.579| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.31 r_work: 0.3691 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34276 Z= 0.119 Angle : 0.588 8.894 46321 Z= 0.291 Chirality : 0.041 0.210 5617 Planarity : 0.003 0.046 5931 Dihedral : 4.555 100.418 4773 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.83 % Allowed : 18.24 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.12), residues: 4407 helix: 1.58 (0.09), residues: 2895 sheet: -0.44 (0.35), residues: 191 loop : -1.13 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 435 HIS 0.010 0.001 HIS z 161 PHE 0.011 0.001 PHE Q 441 TYR 0.018 0.001 TYR a 426 ARG 0.006 0.001 ARG g 518 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 2162) hydrogen bonds : angle 3.82771 ( 6366) covalent geometry : bond 0.00261 (34273) covalent geometry : angle 0.58831 (46321) Misc. bond : bond 0.00070 ( 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: 103 poor density : 861 time to evaluate : 4.852 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: a 20 GLN cc_start: 0.9082 (mt0) cc_final: 0.8440 (mm-40) REVERT: a 110 GLN cc_start: 0.8984 (mt0) cc_final: 0.7801 (mt0) REVERT: a 146 ASP cc_start: 0.5115 (t0) cc_final: 0.4890 (t0) REVERT: a 443 ARG cc_start: 0.8927 (mtm110) cc_final: 0.8508 (ttp-110) REVERT: a 527 ILE cc_start: 0.8869 (mm) cc_final: 0.8627 (mt) REVERT: A 20 GLN cc_start: 0.8814 (mt0) cc_final: 0.8613 (mt0) REVERT: A 51 ASP cc_start: 0.6865 (m-30) cc_final: 0.6596 (m-30) REVERT: A 106 GLU cc_start: 0.7781 (pt0) cc_final: 0.7563 (pt0) REVERT: A 109 LYS cc_start: 0.9145 (mmtp) cc_final: 0.8922 (mmtp) REVERT: A 434 GLU cc_start: 0.8541 (mp0) cc_final: 0.8014 (mp0) REVERT: A 443 ARG cc_start: 0.8715 (mtp-110) cc_final: 0.8471 (ttm-80) REVERT: A 473 GLU cc_start: 0.8311 (tp30) cc_final: 0.8010 (tp30) REVERT: b 49 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7574 (t0) REVERT: b 82 LYS cc_start: 0.9226 (ttmt) cc_final: 0.8672 (tptp) REVERT: b 97 ASP cc_start: 0.6636 (t0) cc_final: 0.5421 (m-30) REVERT: b 120 LYS cc_start: 0.9282 (mtmt) cc_final: 0.8849 (mmtm) REVERT: b 142 LEU cc_start: 0.8912 (tp) cc_final: 0.8585 (tp) REVERT: b 162 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8105 (tt) REVERT: b 445 MET cc_start: 0.8331 (mmp) cc_final: 0.8115 (mmp) REVERT: b 458 SER cc_start: 0.8673 (p) cc_final: 0.8161 (t) REVERT: b 480 MET cc_start: 0.7404 (pmm) cc_final: 0.7085 (mpp) REVERT: B 77 ASP cc_start: 0.7307 (p0) cc_final: 0.6203 (m-30) REVERT: B 91 GLN cc_start: 0.7535 (tp-100) cc_final: 0.7064 (tp40) REVERT: B 120 LYS cc_start: 0.9210 (tttt) cc_final: 0.9003 (tptt) REVERT: D 57 MET cc_start: 0.8914 (mmm) cc_final: 0.8599 (mmt) REVERT: D 138 GLN cc_start: 0.8635 (tp40) cc_final: 0.8356 (tp40) REVERT: D 459 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8482 (mm-30) REVERT: D 472 ASN cc_start: 0.8328 (t0) cc_final: 0.8127 (t0) REVERT: d 46 ASP cc_start: 0.8809 (m-30) cc_final: 0.8579 (m-30) REVERT: d 82 GLN cc_start: 0.7734 (pt0) cc_final: 0.7370 (tm-30) REVERT: E 37 MET cc_start: 0.8588 (mmp) cc_final: 0.8352 (mmp) REVERT: E 79 MET cc_start: 0.8340 (tpp) cc_final: 0.7737 (tpt) REVERT: E 117 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8486 (mm-30) REVERT: e 30 GLU cc_start: 0.8648 (mp0) cc_final: 0.7904 (pp20) REVERT: e 46 MET cc_start: 0.9098 (mmm) cc_final: 0.8842 (mmm) REVERT: e 89 MET cc_start: 0.8680 (mtm) cc_final: 0.8435 (mtm) REVERT: e 442 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: e 463 ASN cc_start: 0.8849 (m-40) cc_final: 0.8496 (m-40) REVERT: e 533 LYS cc_start: 0.7454 (tptm) cc_final: 0.7148 (tptm) REVERT: g 38 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8472 (mtp85) REVERT: g 69 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7862 (mm-30) REVERT: g 124 SER cc_start: 0.9354 (m) cc_final: 0.9134 (p) REVERT: g 454 ASN cc_start: 0.9116 (m-40) cc_final: 0.8737 (m-40) REVERT: g 518 ARG cc_start: 0.8466 (mtp85) cc_final: 0.8019 (mtp85) REVERT: G 47 MET cc_start: 0.8841 (mmm) cc_final: 0.7878 (mmm) REVERT: G 49 MET cc_start: 0.8975 (tpp) cc_final: 0.8663 (mmt) REVERT: G 69 GLU cc_start: 0.6922 (tp30) cc_final: 0.6587 (tm-30) REVERT: G 73 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7588 (pm20) REVERT: G 115 GLN cc_start: 0.7976 (mp10) cc_final: 0.7694 (mp10) REVERT: G 145 ASP cc_start: 0.8052 (t0) cc_final: 0.7303 (m-30) REVERT: h 21 GLN cc_start: 0.7896 (tp40) cc_final: 0.7643 (tm-30) REVERT: h 61 ASP cc_start: 0.8120 (t70) cc_final: 0.7759 (t70) REVERT: h 105 LEU cc_start: 0.9273 (mt) cc_final: 0.9011 (mt) REVERT: h 374 LEU cc_start: 0.7448 (mt) cc_final: 0.7193 (mt) REVERT: h 387 ARG cc_start: 0.7193 (ptm-80) cc_final: 0.6595 (ptm160) REVERT: h 394 MET cc_start: 0.8173 (mmp) cc_final: 0.7865 (mmp) REVERT: h 475 TYR cc_start: 0.7456 (m-80) cc_final: 0.7212 (m-10) REVERT: h 517 ASP cc_start: 0.7427 (t0) cc_final: 0.6970 (t0) REVERT: H 106 LYS cc_start: 0.8580 (tttp) cc_final: 0.8218 (ttpt) REVERT: H 116 LEU cc_start: 0.9049 (tp) cc_final: 0.8771 (mm) REVERT: H 130 GLN cc_start: 0.8000 (mm110) cc_final: 0.7794 (tp-100) REVERT: H 413 GLU cc_start: 0.8594 (mp0) cc_final: 0.8324 (mm-30) REVERT: H 415 GLU cc_start: 0.8536 (tp30) cc_final: 0.8285 (tp30) REVERT: H 455 PHE cc_start: 0.7911 (m-10) cc_final: 0.7676 (m-10) REVERT: Q 14 MET cc_start: 0.4466 (ppp) cc_final: 0.3631 (ptt) REVERT: Q 41 GLN cc_start: 0.8740 (tp40) cc_final: 0.8441 (tp40) REVERT: Q 116 GLU cc_start: 0.7486 (tp30) cc_final: 0.6512 (tp30) REVERT: Q 468 TYR cc_start: 0.9116 (m-10) cc_final: 0.8892 (m-10) REVERT: q 34 GLN cc_start: 0.8242 (tp40) cc_final: 0.7948 (mm110) REVERT: q 41 GLN cc_start: 0.8578 (mm-40) cc_final: 0.7937 (tp-100) REVERT: q 134 ILE cc_start: 0.9052 (mt) cc_final: 0.8825 (mm) REVERT: q 385 MET cc_start: 0.4640 (mtt) cc_final: 0.3444 (ttt) REVERT: Z 35 ARG cc_start: 0.8378 (ptt90) cc_final: 0.8058 (ptp-170) REVERT: Z 85 ASP cc_start: 0.7497 (t0) cc_final: 0.7279 (m-30) REVERT: Z 121 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: Z 453 GLN cc_start: 0.9277 (mt0) cc_final: 0.8792 (mt0) REVERT: Z 462 THR cc_start: 0.9300 (m) cc_final: 0.9046 (t) REVERT: Z 487 MET cc_start: 0.8428 (tmm) cc_final: 0.8165 (ppp) REVERT: Z 514 ASN cc_start: 0.8909 (m-40) cc_final: 0.8286 (t0) REVERT: Z 520 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7887 (tm-30) REVERT: Z 521 ILE cc_start: 0.8772 (mt) cc_final: 0.8416 (mt) REVERT: Z 526 MET cc_start: 0.2965 (ttt) cc_final: 0.2297 (tmm) REVERT: z 23 ASN cc_start: 0.8374 (m-40) cc_final: 0.8043 (m-40) REVERT: z 520 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8120 (mm-30) outliers start: 103 outliers final: 56 residues processed: 921 average time/residue: 0.4836 time to fit residues: 716.7382 Evaluate side-chains 833 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 772 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 ILE 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 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 413 SER Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain D residue 489 LYS 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 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 516 LEU 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 117 MET Chi-restraints excluded: chain G residue 128 LYS 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 479 ILE 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 210 SER Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain q residue 524 ILE 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 496 ASP Chi-restraints excluded: chain z residue 25 SER Chi-restraints excluded: chain z residue 34 LEU Chi-restraints excluded: chain z residue 61 ASN Chi-restraints excluded: chain z residue 406 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 143 optimal weight: 4.9990 chunk 429 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 435 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 229 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 279 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 110 GLN ** a 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN b 453 ASN b 502 GLN D 37 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 GLN d 165 ASN h 21 GLN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 59 HIS Z 65 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.123165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.107546 restraints weight = 75897.129| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 3.29 r_work: 0.3538 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.6771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 34276 Z= 0.223 Angle : 0.700 10.042 46321 Z= 0.351 Chirality : 0.045 0.229 5617 Planarity : 0.004 0.072 5931 Dihedral : 5.142 92.800 4773 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.12 % Allowed : 18.41 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.12), residues: 4407 helix: 1.52 (0.09), residues: 2889 sheet: -0.16 (0.34), residues: 209 loop : -1.30 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 435 HIS 0.007 0.001 HIS D 484 PHE 0.015 0.002 PHE A 8 TYR 0.020 0.002 TYR a 426 ARG 0.008 0.001 ARG e 181 Details of bonding type rmsd hydrogen bonds : bond 0.04874 ( 2162) hydrogen bonds : angle 4.11152 ( 6366) covalent geometry : bond 0.00509 (34273) covalent geometry : angle 0.70017 (46321) Misc. bond : bond 0.00164 ( 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: 150 poor density : 793 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 99 GLU cc_start: 0.8318 (tp30) cc_final: 0.8040 (tp30) REVERT: a 106 GLU cc_start: 0.7847 (tp30) cc_final: 0.7541 (tp30) REVERT: a 440 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8484 (mm-30) REVERT: a 443 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7898 (ttp80) REVERT: A 51 ASP cc_start: 0.7824 (m-30) cc_final: 0.7600 (m-30) REVERT: A 105 ASP cc_start: 0.8550 (t70) cc_final: 0.8205 (t0) REVERT: A 109 LYS cc_start: 0.9126 (mmtp) cc_final: 0.8668 (mmtp) REVERT: A 110 GLN cc_start: 0.8520 (mp10) cc_final: 0.8138 (mp10) REVERT: A 440 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7826 (mm-30) REVERT: A 443 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.7978 (ttp-110) REVERT: A 473 GLU cc_start: 0.8603 (tp30) cc_final: 0.8399 (tp30) REVERT: b 49 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7968 (t0) REVERT: b 53 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7664 (pp) REVERT: b 82 LYS cc_start: 0.9220 (ttmt) cc_final: 0.8694 (tptp) REVERT: b 97 ASP cc_start: 0.6068 (t0) cc_final: 0.5002 (m-30) REVERT: b 120 LYS cc_start: 0.9480 (mtmt) cc_final: 0.9071 (mmtm) REVERT: b 142 LEU cc_start: 0.8839 (tp) cc_final: 0.8540 (tp) REVERT: b 162 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8568 (tt) REVERT: b 408 TYR cc_start: 0.8522 (m-80) cc_final: 0.8190 (m-10) REVERT: b 453 ASN cc_start: 0.8994 (m-40) cc_final: 0.8742 (m110) REVERT: b 456 TYR cc_start: 0.8130 (m-10) cc_final: 0.7632 (m-10) REVERT: b 502 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8327 (tp40) REVERT: B 43 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8951 (mm) REVERT: B 66 ASP cc_start: 0.7940 (t0) cc_final: 0.7692 (t0) REVERT: B 91 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7760 (tp-100) REVERT: B 417 MET cc_start: 0.8804 (mtt) cc_final: 0.8520 (mtt) REVERT: B 452 ASP cc_start: 0.8330 (m-30) cc_final: 0.7676 (m-30) REVERT: B 522 LYS cc_start: 0.8273 (mttt) cc_final: 0.7850 (ptpp) REVERT: D 32 GLN cc_start: 0.8482 (pt0) cc_final: 0.8166 (pm20) REVERT: D 57 MET cc_start: 0.9002 (mmm) cc_final: 0.8465 (mmm) REVERT: D 82 GLN cc_start: 0.7643 (mm110) cc_final: 0.6966 (pt0) REVERT: D 472 ASN cc_start: 0.8416 (t0) cc_final: 0.8183 (t0) REVERT: d 49 ARG cc_start: 0.8977 (ptm-80) cc_final: 0.8590 (ttp80) REVERT: E 79 MET cc_start: 0.8482 (tpp) cc_final: 0.7908 (tpt) REVERT: E 117 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8409 (mm-30) REVERT: E 524 MET cc_start: 0.8738 (tpp) cc_final: 0.8400 (tpp) REVERT: e 442 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: e 447 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7989 (mtm180) REVERT: e 463 ASN cc_start: 0.9085 (m-40) cc_final: 0.8666 (m110) REVERT: g 38 ARG cc_start: 0.8924 (mmm-85) cc_final: 0.8441 (mtp85) REVERT: g 69 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8128 (mm-30) REVERT: g 71 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7929 (mp10) REVERT: g 124 SER cc_start: 0.9425 (m) cc_final: 0.9166 (p) REVERT: g 488 VAL cc_start: 0.9305 (OUTLIER) cc_final: 0.9105 (m) REVERT: G 20 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6135 (ttp80) REVERT: G 38 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.7545 (tmm-80) REVERT: G 47 MET cc_start: 0.8893 (mmm) cc_final: 0.8496 (mmm) REVERT: G 59 MET cc_start: 0.8520 (mmt) cc_final: 0.7948 (mmt) REVERT: G 69 GLU cc_start: 0.7223 (tp30) cc_final: 0.7001 (tm-30) REVERT: G 73 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7668 (pm20) REVERT: G 415 GLU cc_start: 0.8513 (mp0) cc_final: 0.7939 (mp0) REVERT: h 45 MET cc_start: 0.8360 (mmm) cc_final: 0.8111 (mpp) REVERT: h 61 ASP cc_start: 0.8221 (t70) cc_final: 0.7875 (t70) REVERT: h 105 LEU cc_start: 0.9425 (mt) cc_final: 0.9064 (mt) REVERT: h 374 LEU cc_start: 0.7661 (mt) cc_final: 0.7170 (mt) REVERT: h 382 MET cc_start: 0.4801 (mmp) cc_final: 0.4301 (mmp) REVERT: h 387 ARG cc_start: 0.7283 (ptm-80) cc_final: 0.6847 (ptm160) REVERT: h 388 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7494 (p) REVERT: h 443 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8384 (mt-10) REVERT: h 497 MET cc_start: 0.8785 (mmm) cc_final: 0.8401 (mmm) REVERT: h 508 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: h 511 CYS cc_start: 0.8610 (m) cc_final: 0.8384 (m) REVERT: H 25 ASN cc_start: 0.9259 (m-40) cc_final: 0.8989 (m-40) REVERT: H 45 MET cc_start: 0.7767 (ttm) cc_final: 0.7290 (ttt) REVERT: H 79 LEU cc_start: 0.8516 (mt) cc_final: 0.8265 (mp) REVERT: H 96 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8527 (t) REVERT: H 106 LYS cc_start: 0.8737 (tttp) cc_final: 0.8309 (ttpt) REVERT: H 413 GLU cc_start: 0.8841 (mp0) cc_final: 0.8635 (mm-30) REVERT: H 415 GLU cc_start: 0.8901 (tp30) cc_final: 0.8604 (tp30) REVERT: H 422 ASP cc_start: 0.8789 (m-30) cc_final: 0.8267 (p0) REVERT: H 501 ASN cc_start: 0.8350 (m-40) cc_final: 0.8109 (m-40) REVERT: Q 14 MET cc_start: 0.4155 (ppp) cc_final: 0.3319 (ptm) REVERT: Q 31 ARG cc_start: 0.7865 (mmt180) cc_final: 0.7448 (mmt-90) REVERT: Q 38 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8311 (pt0) REVERT: Q 41 GLN cc_start: 0.8909 (tp40) cc_final: 0.8570 (tp40) REVERT: Q 79 GLN cc_start: 0.8533 (mp10) cc_final: 0.8196 (mp10) REVERT: Q 116 GLU cc_start: 0.7747 (tp30) cc_final: 0.7003 (tp30) REVERT: q 41 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8370 (tp40) REVERT: q 55 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8760 (mtm) REVERT: q 385 MET cc_start: 0.4932 (mtt) cc_final: 0.3546 (ttt) REVERT: Z 79 LYS cc_start: 0.8643 (mmtp) cc_final: 0.8404 (mmtt) REVERT: Z 85 ASP cc_start: 0.8149 (t0) cc_final: 0.7428 (t0) REVERT: Z 95 ASN cc_start: 0.9059 (t0) cc_final: 0.8833 (t0) REVERT: Z 442 ASP cc_start: 0.8326 (m-30) cc_final: 0.8087 (m-30) REVERT: Z 453 GLN cc_start: 0.9275 (mt0) cc_final: 0.8982 (mt0) REVERT: Z 458 ASP cc_start: 0.8205 (t0) cc_final: 0.6951 (t0) REVERT: Z 467 GLN cc_start: 0.8950 (mt0) cc_final: 0.8481 (mm-40) REVERT: Z 487 MET cc_start: 0.8620 (tmm) cc_final: 0.8227 (ppp) REVERT: Z 520 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7572 (tm-30) REVERT: z 23 ASN cc_start: 0.8596 (m-40) cc_final: 0.8121 (m110) REVERT: z 46 MET cc_start: 0.7986 (ttm) cc_final: 0.7785 (ttm) REVERT: z 520 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8213 (mm-30) outliers start: 150 outliers final: 82 residues processed: 889 average time/residue: 0.5305 time to fit residues: 755.2132 Evaluate side-chains 793 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 696 time to evaluate : 3.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 61 ILE 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 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 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 125 THR Chi-restraints excluded: chain b residue 162 ILE 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 502 GLN Chi-restraints excluded: chain B residue 43 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 B residue 519 ASN 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 504 LEU Chi-restraints excluded: chain d residue 537 ASN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 80 ASP 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 e residue 525 ILE Chi-restraints excluded: chain g residue 31 LYS 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 488 VAL 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 36 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 169 SER 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 477 VAL Chi-restraints excluded: chain h residue 508 GLU 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 427 ILE 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 126 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 55 MET Chi-restraints excluded: chain q residue 210 SER Chi-restraints excluded: chain q residue 406 LYS Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain Z residue 65 HIS 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 132 GLN 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 47 LEU Chi-restraints excluded: chain z residue 61 ASN Chi-restraints excluded: chain z residue 198 HIS 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 213 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 357 optimal weight: 6.9990 chunk 142 optimal weight: 1.9990 chunk 304 optimal weight: 0.1980 chunk 52 optimal weight: 7.9990 chunk 331 optimal weight: 5.9990 chunk 324 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 482 ASN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN b 391 HIS b 502 GLN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 484 ASN E 493 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 462 ASN ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.124539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.108885 restraints weight = 76761.724| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.38 r_work: 0.3555 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.7076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34276 Z= 0.148 Angle : 0.637 10.513 46321 Z= 0.315 Chirality : 0.042 0.289 5617 Planarity : 0.004 0.045 5931 Dihedral : 4.902 95.998 4773 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.38 % Allowed : 20.00 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.13), residues: 4407 helix: 1.69 (0.09), residues: 2910 sheet: -0.43 (0.36), residues: 187 loop : -1.20 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 435 HIS 0.010 0.001 HIS b 391 PHE 0.029 0.001 PHE q 103 TYR 0.027 0.002 TYR q 505 ARG 0.011 0.001 ARG z 432 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 2162) hydrogen bonds : angle 3.89507 ( 6366) covalent geometry : bond 0.00339 (34273) covalent geometry : angle 0.63737 (46321) Misc. bond : bond 0.00088 ( 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 896 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 773 time to evaluate : 3.887 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: a 20 GLN cc_start: 0.9107 (mt0) cc_final: 0.8427 (mm-40) REVERT: a 99 GLU cc_start: 0.8340 (tp30) cc_final: 0.7926 (tp30) REVERT: a 106 GLU cc_start: 0.7832 (tp30) cc_final: 0.7526 (tp30) REVERT: A 51 ASP cc_start: 0.7656 (m-30) cc_final: 0.7392 (m-30) REVERT: A 105 ASP cc_start: 0.8493 (t70) cc_final: 0.8144 (t0) REVERT: A 440 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7821 (mm-30) REVERT: A 443 ARG cc_start: 0.8604 (mtp-110) cc_final: 0.7962 (ttp-110) REVERT: A 473 GLU cc_start: 0.8625 (tp30) cc_final: 0.8404 (tp30) REVERT: b 49 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7674 (t0) REVERT: b 82 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8710 (tptp) REVERT: b 97 ASP cc_start: 0.5973 (t0) cc_final: 0.5011 (m-30) REVERT: b 111 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8373 (ptp-110) REVERT: b 120 LYS cc_start: 0.9429 (mtmt) cc_final: 0.9072 (mmtm) REVERT: b 162 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8409 (tt) REVERT: b 441 LYS cc_start: 0.8956 (mptt) cc_final: 0.8476 (mptt) REVERT: b 502 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: B 43 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8912 (mm) REVERT: B 431 LYS cc_start: 0.8217 (mmmt) cc_final: 0.8000 (mttt) REVERT: B 488 MET cc_start: 0.3102 (ppp) cc_final: 0.2865 (mmm) REVERT: B 522 LYS cc_start: 0.8435 (mttt) cc_final: 0.7995 (ptpp) REVERT: D 57 MET cc_start: 0.8932 (mmm) cc_final: 0.8336 (mmm) REVERT: D 82 GLN cc_start: 0.7496 (mm110) cc_final: 0.7149 (pt0) REVERT: D 459 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8480 (mm-30) REVERT: D 472 ASN cc_start: 0.8473 (t0) cc_final: 0.8241 (t0) REVERT: d 65 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8132 (mmtt) REVERT: d 81 MET cc_start: 0.8260 (mmm) cc_final: 0.8001 (mmm) REVERT: d 90 MET cc_start: 0.8331 (mtm) cc_final: 0.7827 (mtp) REVERT: d 481 ARG cc_start: 0.9086 (ttp-110) cc_final: 0.8635 (ttp-170) REVERT: E 30 GLU cc_start: 0.8085 (pm20) cc_final: 0.7702 (pm20) REVERT: E 79 MET cc_start: 0.8485 (tpp) cc_final: 0.7858 (tpt) REVERT: E 524 MET cc_start: 0.8837 (tpp) cc_final: 0.8417 (tpp) REVERT: e 46 MET cc_start: 0.9276 (mmm) cc_final: 0.8986 (mmm) REVERT: e 92 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8000 (tp) REVERT: e 442 GLU cc_start: 0.7923 (tt0) cc_final: 0.7478 (tt0) REVERT: e 463 ASN cc_start: 0.9043 (m-40) cc_final: 0.8594 (m110) REVERT: g 38 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.8306 (ttp80) REVERT: g 69 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8119 (mm-30) REVERT: g 71 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7947 (mp10) REVERT: g 124 SER cc_start: 0.9393 (m) cc_final: 0.9154 (p) REVERT: G 20 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.6258 (ttp80) REVERT: G 38 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7492 (tmm-80) REVERT: G 47 MET cc_start: 0.8958 (mmm) cc_final: 0.8363 (mmm) REVERT: G 59 MET cc_start: 0.8571 (mmt) cc_final: 0.7813 (mmt) REVERT: G 69 GLU cc_start: 0.7710 (tp30) cc_final: 0.7340 (tm-30) REVERT: G 115 GLN cc_start: 0.8106 (mp10) cc_final: 0.7823 (mp10) REVERT: G 415 GLU cc_start: 0.8498 (mp0) cc_final: 0.8203 (mp0) REVERT: G 489 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7375 (t70) REVERT: h 45 MET cc_start: 0.8381 (mmm) cc_final: 0.8180 (mpp) REVERT: h 61 ASP cc_start: 0.8163 (t70) cc_final: 0.7853 (t70) REVERT: h 105 LEU cc_start: 0.9401 (mt) cc_final: 0.9075 (mt) REVERT: h 387 ARG cc_start: 0.7351 (ptm-80) cc_final: 0.7003 (ptm160) REVERT: h 388 SER cc_start: 0.7822 (OUTLIER) cc_final: 0.7502 (p) REVERT: h 443 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8234 (mt-10) REVERT: h 475 TYR cc_start: 0.7578 (m-80) cc_final: 0.7339 (m-10) REVERT: h 497 MET cc_start: 0.8727 (mmm) cc_final: 0.8415 (mmm) REVERT: h 508 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8390 (mp0) REVERT: h 511 CYS cc_start: 0.8722 (m) cc_final: 0.8511 (m) REVERT: H 103 GLU cc_start: 0.8317 (tp30) cc_final: 0.7965 (tp30) REVERT: H 106 LYS cc_start: 0.8690 (tttp) cc_final: 0.8175 (ttpt) REVERT: Q 14 MET cc_start: 0.4619 (ppp) cc_final: 0.3831 (ptt) REVERT: Q 31 ARG cc_start: 0.7849 (mmt180) cc_final: 0.7421 (mmt-90) REVERT: Q 38 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8330 (pt0) REVERT: Q 41 GLN cc_start: 0.8830 (tp40) cc_final: 0.8467 (tp40) REVERT: Q 79 GLN cc_start: 0.8500 (mp10) cc_final: 0.8195 (mp10) REVERT: Q 90 SER cc_start: 0.9449 (OUTLIER) cc_final: 0.9111 (p) REVERT: Q 116 GLU cc_start: 0.7677 (tp30) cc_final: 0.6726 (tp30) REVERT: Q 120 ARG cc_start: 0.8792 (mpt-90) cc_final: 0.7981 (mmt180) REVERT: q 41 GLN cc_start: 0.8785 (mm-40) cc_final: 0.8305 (tp-100) REVERT: q 385 MET cc_start: 0.5005 (mtt) cc_final: 0.3700 (ttt) REVERT: q 526 MET cc_start: 0.7957 (mpp) cc_final: 0.7499 (mmm) REVERT: Z 59 ASP cc_start: 0.7626 (t70) cc_final: 0.7348 (t0) REVERT: Z 66 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7792 (mm-30) REVERT: Z 124 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8175 (pp20) REVERT: Z 442 ASP cc_start: 0.8346 (m-30) cc_final: 0.8031 (m-30) REVERT: Z 453 GLN cc_start: 0.9215 (mt0) cc_final: 0.8920 (mt0) REVERT: Z 467 GLN cc_start: 0.8835 (mt0) cc_final: 0.8461 (mm-40) REVERT: Z 487 MET cc_start: 0.8620 (tmm) cc_final: 0.8246 (ppp) REVERT: Z 520 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7783 (tm-30) REVERT: z 520 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8138 (mm-30) outliers start: 123 outliers final: 67 residues processed: 851 average time/residue: 0.4841 time to fit residues: 667.4696 Evaluate side-chains 791 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 711 time to evaluate : 4.142 ------------------------------------------------------------------------------- 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 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 162 ILE Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain b residue 502 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 43 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 485 ILE Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 80 GLN 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 441 LEU Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 129 ILE 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 22 VAL Chi-restraints excluded: chain g residue 59 MET 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 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 489 ASP Chi-restraints excluded: chain G residue 497 GLU 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 508 GLU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 479 ILE 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 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 q residue 497 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 112 GLU Chi-restraints excluded: chain Z residue 132 GLN 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 61 ASN Chi-restraints excluded: chain z residue 406 CYS 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 177 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 434 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 230 optimal weight: 6.9990 chunk 414 optimal weight: 0.0060 chunk 113 optimal weight: 0.4980 chunk 144 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS b 453 ASN b 502 GLN D 468 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN Z 454 ASN z 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.125460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109908 restraints weight = 76454.356| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.42 r_work: 0.3568 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 34276 Z= 0.128 Angle : 0.629 15.155 46321 Z= 0.310 Chirality : 0.041 0.215 5617 Planarity : 0.003 0.044 5931 Dihedral : 4.783 97.497 4773 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.13 % Allowed : 21.13 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.13), residues: 4407 helix: 1.83 (0.10), residues: 2898 sheet: -0.42 (0.35), residues: 199 loop : -1.11 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 435 HIS 0.010 0.001 HIS b 391 PHE 0.016 0.001 PHE q 103 TYR 0.021 0.001 TYR q 505 ARG 0.007 0.000 ARG z 28 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 2162) hydrogen bonds : angle 3.81879 ( 6366) covalent geometry : bond 0.00293 (34273) covalent geometry : angle 0.62940 (46321) Misc. bond : bond 0.00088 ( 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 873 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 759 time to evaluate : 4.574 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: a 20 GLN cc_start: 0.9071 (mt0) cc_final: 0.8413 (mm-40) REVERT: a 95 ILE cc_start: 0.9340 (pt) cc_final: 0.8993 (mt) REVERT: a 99 GLU cc_start: 0.8347 (tp30) cc_final: 0.7940 (tp30) REVERT: a 106 GLU cc_start: 0.8000 (tp30) cc_final: 0.7666 (tp30) REVERT: a 443 ARG cc_start: 0.8962 (mtm110) cc_final: 0.8741 (ttp80) REVERT: A 51 ASP cc_start: 0.7567 (m-30) cc_final: 0.7287 (m-30) REVERT: A 105 ASP cc_start: 0.8527 (t70) cc_final: 0.8191 (t0) REVERT: A 106 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: A 109 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8382 (mmtp) REVERT: A 110 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8027 (mp10) REVERT: A 430 MET cc_start: 0.7775 (tpt) cc_final: 0.7569 (tpt) REVERT: A 434 GLU cc_start: 0.8696 (mp0) cc_final: 0.8035 (mp0) REVERT: A 440 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 443 ARG cc_start: 0.8592 (mtp-110) cc_final: 0.7982 (ttp-110) REVERT: A 473 GLU cc_start: 0.8588 (tp30) cc_final: 0.8360 (tp30) REVERT: b 49 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7606 (t0) REVERT: b 53 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7458 (pp) REVERT: b 82 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8496 (tptp) REVERT: b 91 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7657 (tp40) REVERT: b 97 ASP cc_start: 0.5883 (t0) cc_final: 0.5161 (m-30) REVERT: b 111 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.8375 (ptp-110) REVERT: b 120 LYS cc_start: 0.9438 (mtmt) cc_final: 0.9097 (mmtm) REVERT: b 502 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.8097 (tt0) REVERT: B 91 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7459 (tp40) REVERT: B 438 SER cc_start: 0.9442 (OUTLIER) cc_final: 0.8990 (p) REVERT: B 522 LYS cc_start: 0.8430 (mttt) cc_final: 0.8004 (ptpp) REVERT: D 57 MET cc_start: 0.8851 (mmm) cc_final: 0.8378 (mmm) REVERT: D 459 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8484 (mm-30) REVERT: D 472 ASN cc_start: 0.8447 (t0) cc_final: 0.8233 (t0) REVERT: D 489 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.8035 (tmtt) REVERT: D 504 LEU cc_start: 0.6804 (mt) cc_final: 0.6603 (mt) REVERT: d 49 ARG cc_start: 0.8936 (ptm-80) cc_final: 0.8538 (ttp80) REVERT: d 481 ARG cc_start: 0.9014 (ttp-110) cc_final: 0.8789 (ttp-170) REVERT: E 79 MET cc_start: 0.8442 (tpp) cc_final: 0.7761 (tpt) REVERT: E 444 TYR cc_start: 0.8301 (m-80) cc_final: 0.8080 (m-10) REVERT: E 470 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7934 (tm-30) REVERT: E 524 MET cc_start: 0.8829 (tpp) cc_final: 0.8450 (tpp) REVERT: e 89 MET cc_start: 0.9036 (mtm) cc_final: 0.8704 (mtt) REVERT: e 442 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: e 463 ASN cc_start: 0.9012 (m-40) cc_final: 0.8576 (m110) REVERT: g 38 ARG cc_start: 0.8903 (mmm-85) cc_final: 0.8390 (ttp80) REVERT: g 69 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8110 (mm-30) REVERT: g 71 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7934 (mp10) REVERT: G 20 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6572 (ttp80) REVERT: G 38 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.7428 (tmm-80) REVERT: G 47 MET cc_start: 0.8934 (mmm) cc_final: 0.8311 (mmm) REVERT: G 59 MET cc_start: 0.8503 (mmt) cc_final: 0.7849 (mmt) REVERT: G 69 GLU cc_start: 0.7610 (tp30) cc_final: 0.7262 (tm-30) REVERT: G 115 GLN cc_start: 0.8135 (mp10) cc_final: 0.7850 (mp10) REVERT: G 415 GLU cc_start: 0.8453 (mp0) cc_final: 0.8173 (mp0) REVERT: G 489 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7418 (t70) REVERT: h 45 MET cc_start: 0.8411 (mmm) cc_final: 0.8205 (mpp) REVERT: h 61 ASP cc_start: 0.8166 (t70) cc_final: 0.7901 (t70) REVERT: h 105 LEU cc_start: 0.9404 (mt) cc_final: 0.9090 (mt) REVERT: h 387 ARG cc_start: 0.7341 (ptm-80) cc_final: 0.6977 (ptm160) REVERT: h 394 MET cc_start: 0.8201 (mmp) cc_final: 0.7930 (mmp) REVERT: h 475 TYR cc_start: 0.7531 (m-80) cc_final: 0.7303 (m-10) REVERT: h 497 MET cc_start: 0.8699 (mmm) cc_final: 0.8435 (mmm) REVERT: h 508 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: h 511 CYS cc_start: 0.8764 (m) cc_final: 0.8545 (m) REVERT: H 45 MET cc_start: 0.7779 (ttm) cc_final: 0.7204 (ttt) REVERT: H 103 GLU cc_start: 0.8376 (tp30) cc_final: 0.8104 (tp30) REVERT: H 106 LYS cc_start: 0.8705 (tttp) cc_final: 0.8159 (ttpt) REVERT: Q 14 MET cc_start: 0.4365 (ppp) cc_final: 0.3680 (ptt) REVERT: Q 38 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8374 (pt0) REVERT: Q 41 GLN cc_start: 0.8738 (tp40) cc_final: 0.8343 (tp40) REVERT: Q 79 GLN cc_start: 0.8503 (mp10) cc_final: 0.8195 (mp10) REVERT: Q 90 SER cc_start: 0.9415 (OUTLIER) cc_final: 0.9075 (p) REVERT: Q 116 GLU cc_start: 0.7643 (tp30) cc_final: 0.6710 (tp30) REVERT: Q 120 ARG cc_start: 0.8784 (mpt-90) cc_final: 0.7959 (mmt180) REVERT: q 41 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8295 (tp-100) REVERT: q 55 MET cc_start: 0.8883 (mtm) cc_final: 0.8533 (mtm) REVERT: q 74 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8359 (tmm-80) REVERT: q 385 MET cc_start: 0.4510 (mtt) cc_final: 0.3444 (ttt) REVERT: Z 35 ARG cc_start: 0.8569 (ptm160) cc_final: 0.8244 (ptp-170) REVERT: Z 442 ASP cc_start: 0.8366 (m-30) cc_final: 0.8031 (m-30) REVERT: Z 467 GLN cc_start: 0.8757 (mt0) cc_final: 0.8459 (mm-40) REVERT: Z 487 MET cc_start: 0.8669 (tmm) cc_final: 0.8370 (ppp) REVERT: Z 520 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7709 (tm-30) REVERT: z 23 ASN cc_start: 0.8498 (m110) cc_final: 0.8145 (m-40) REVERT: z 46 MET cc_start: 0.8185 (ttm) cc_final: 0.7984 (ttm) REVERT: z 388 LYS cc_start: 0.7141 (tptt) cc_final: 0.6936 (tppt) REVERT: z 406 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7170 (p) REVERT: z 520 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8116 (mm-30) outliers start: 114 outliers final: 69 residues processed: 831 average time/residue: 0.4733 time to fit residues: 633.6121 Evaluate side-chains 788 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 704 time to evaluate : 3.489 ------------------------------------------------------------------------------- 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 106 GLU 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 111 ARG Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 502 GLN Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 438 SER 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 489 LYS 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 29 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 129 ILE 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 499 MET Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 422 LEU 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 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 117 MET Chi-restraints excluded: chain G residue 489 ASP Chi-restraints excluded: chain G residue 497 GLU 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 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 427 ILE 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 95 GLN 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 480 LEU Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain Z residue 67 MET 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 112 GLU Chi-restraints excluded: chain Z residue 132 GLN 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 61 ASN Chi-restraints excluded: chain z residue 406 CYS 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 18 optimal weight: 6.9990 chunk 356 optimal weight: 4.9990 chunk 400 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 391 HIS b 502 GLN D 468 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 493 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.124409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109392 restraints weight = 75964.853| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.18 r_work: 0.3564 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.7423 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= 0.142 Angle : 0.653 16.202 46321 Z= 0.320 Chirality : 0.042 0.243 5617 Planarity : 0.004 0.087 5931 Dihedral : 4.805 96.797 4773 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.02 % Allowed : 21.29 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.13), residues: 4407 helix: 1.88 (0.09), residues: 2902 sheet: -0.39 (0.35), residues: 199 loop : -1.13 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 435 HIS 0.010 0.001 HIS b 391 PHE 0.018 0.001 PHE q 103 TYR 0.022 0.001 TYR H 423 ARG 0.010 0.000 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 2162) hydrogen bonds : angle 3.83009 ( 6366) covalent geometry : bond 0.00325 (34273) covalent geometry : angle 0.65338 (46321) Misc. bond : bond 0.00093 ( 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 852 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 742 time to evaluate : 5.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 95 ILE cc_start: 0.9359 (pt) cc_final: 0.9030 (mt) REVERT: a 99 GLU cc_start: 0.8328 (tp30) cc_final: 0.7902 (tp30) REVERT: a 106 GLU cc_start: 0.8079 (tp30) cc_final: 0.7724 (tp30) REVERT: a 443 ARG cc_start: 0.8953 (mtm110) cc_final: 0.8721 (ttp80) REVERT: A 51 ASP cc_start: 0.7528 (m-30) cc_final: 0.7255 (m-30) REVERT: A 105 ASP cc_start: 0.8449 (t70) cc_final: 0.8172 (t0) REVERT: A 109 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8439 (mmtp) REVERT: A 440 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 443 ARG cc_start: 0.8611 (mtp-110) cc_final: 0.7955 (ttp-110) REVERT: A 473 GLU cc_start: 0.8576 (tp30) cc_final: 0.8364 (tp30) REVERT: b 49 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7600 (t0) REVERT: b 53 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7331 (pp) REVERT: b 82 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8566 (tptp) REVERT: b 91 GLN cc_start: 0.8001 (tp-100) cc_final: 0.7769 (tp40) REVERT: b 97 ASP cc_start: 0.5969 (t0) cc_final: 0.5136 (m-30) REVERT: b 111 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8329 (ptp-110) REVERT: b 120 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9149 (mmtm) REVERT: b 426 ASN cc_start: 0.8189 (m-40) cc_final: 0.7966 (m-40) REVERT: b 441 LYS cc_start: 0.8972 (mptt) cc_final: 0.8455 (mptt) REVERT: b 453 ASN cc_start: 0.8889 (m-40) cc_final: 0.8623 (m-40) REVERT: b 460 ASP cc_start: 0.8622 (t0) cc_final: 0.8343 (t0) REVERT: B 120 LYS cc_start: 0.9486 (mmmt) cc_final: 0.9178 (mmmt) REVERT: B 438 SER cc_start: 0.9449 (OUTLIER) cc_final: 0.9044 (p) REVERT: B 522 LYS cc_start: 0.8437 (mttt) cc_final: 0.8010 (ptpp) REVERT: D 32 GLN cc_start: 0.8546 (pt0) cc_final: 0.8154 (pm20) REVERT: D 57 MET cc_start: 0.8911 (mmm) cc_final: 0.8459 (mmm) REVERT: D 459 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8415 (mm-30) REVERT: D 472 ASN cc_start: 0.8490 (t0) cc_final: 0.8269 (t0) REVERT: D 504 LEU cc_start: 0.6822 (mt) cc_final: 0.6612 (mt) REVERT: d 49 ARG cc_start: 0.8902 (ptm-80) cc_final: 0.8550 (ttp80) REVERT: d 90 MET cc_start: 0.8510 (mtp) cc_final: 0.8309 (mtm) REVERT: E 30 GLU cc_start: 0.8153 (pm20) cc_final: 0.7812 (pm20) REVERT: E 79 MET cc_start: 0.8466 (tpp) cc_final: 0.7891 (tpt) REVERT: E 442 GLU cc_start: 0.7692 (mp0) cc_final: 0.7288 (mp0) REVERT: E 454 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8085 (mt-10) REVERT: E 470 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 524 MET cc_start: 0.8867 (tpp) cc_final: 0.8458 (tpp) REVERT: e 89 MET cc_start: 0.8990 (mtm) cc_final: 0.8685 (mtt) REVERT: e 442 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: g 38 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8373 (ttp80) REVERT: g 69 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8046 (mm-30) REVERT: g 71 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7980 (mp10) REVERT: G 20 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6558 (ttp80) REVERT: G 38 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7425 (tmm-80) REVERT: G 45 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8904 (p) REVERT: G 47 MET cc_start: 0.8959 (mmm) cc_final: 0.8305 (mmm) REVERT: G 59 MET cc_start: 0.8467 (mmt) cc_final: 0.7853 (mmt) REVERT: G 69 GLU cc_start: 0.7472 (tp30) cc_final: 0.7181 (tm-30) REVERT: G 115 GLN cc_start: 0.8131 (mp10) cc_final: 0.7847 (mp10) REVERT: G 415 GLU cc_start: 0.8411 (mp0) cc_final: 0.8144 (mp0) REVERT: G 489 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7515 (t70) REVERT: h 61 ASP cc_start: 0.8317 (t70) cc_final: 0.8029 (t70) REVERT: h 105 LEU cc_start: 0.9410 (mt) cc_final: 0.9092 (mt) REVERT: h 387 ARG cc_start: 0.7266 (ptm-80) cc_final: 0.6910 (ptm160) REVERT: h 394 MET cc_start: 0.8203 (mmp) cc_final: 0.7928 (mmp) REVERT: h 443 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8192 (mt-10) REVERT: h 475 TYR cc_start: 0.7713 (m-80) cc_final: 0.7474 (m-10) REVERT: h 497 MET cc_start: 0.8678 (mmm) cc_final: 0.8432 (mmm) REVERT: h 508 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8353 (mp0) REVERT: h 511 CYS cc_start: 0.8753 (m) cc_final: 0.8527 (m) REVERT: H 99 LEU cc_start: 0.9256 (mp) cc_final: 0.9014 (mp) REVERT: H 103 GLU cc_start: 0.8403 (tp30) cc_final: 0.8125 (tp30) REVERT: H 106 LYS cc_start: 0.8740 (tttp) cc_final: 0.8192 (ttpt) REVERT: H 455 PHE cc_start: 0.8450 (m-80) cc_final: 0.8240 (m-80) REVERT: H 521 LYS cc_start: 0.8296 (ttpp) cc_final: 0.7692 (tmtt) REVERT: Q 14 MET cc_start: 0.4667 (ppp) cc_final: 0.4065 (mtm) REVERT: Q 38 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8328 (pt0) REVERT: Q 41 GLN cc_start: 0.8745 (tp40) cc_final: 0.8384 (tp40) REVERT: Q 79 GLN cc_start: 0.8542 (mp10) cc_final: 0.8210 (mp10) REVERT: Q 116 GLU cc_start: 0.7681 (tp30) cc_final: 0.6764 (tp30) REVERT: Q 120 ARG cc_start: 0.8723 (mpt-90) cc_final: 0.7828 (mmt180) REVERT: q 41 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8242 (tp-100) REVERT: q 74 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8371 (tmm-80) REVERT: q 385 MET cc_start: 0.4675 (mtt) cc_final: 0.3638 (ttt) REVERT: q 526 MET cc_start: 0.7880 (mpp) cc_final: 0.7507 (mmm) REVERT: Z 61 ASN cc_start: 0.8724 (p0) cc_final: 0.8271 (p0) REVERT: Z 442 ASP cc_start: 0.8350 (m-30) cc_final: 0.8003 (m-30) REVERT: Z 462 THR cc_start: 0.9321 (m) cc_final: 0.9000 (t) REVERT: Z 467 GLN cc_start: 0.8801 (mt0) cc_final: 0.8565 (mm-40) REVERT: Z 487 MET cc_start: 0.8676 (tmm) cc_final: 0.8373 (ppp) REVERT: Z 520 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7687 (tm-30) REVERT: Z 522 MET cc_start: 0.7378 (tpt) cc_final: 0.7153 (tpt) REVERT: z 23 ASN cc_start: 0.8483 (m110) cc_final: 0.7996 (m-40) REVERT: z 35 ARG cc_start: 0.8906 (ptm160) cc_final: 0.8657 (ptm160) REVERT: z 388 LYS cc_start: 0.7222 (tptt) cc_final: 0.6982 (tppt) outliers start: 110 outliers final: 75 residues processed: 816 average time/residue: 0.5549 time to fit residues: 727.3045 Evaluate side-chains 779 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 694 time to evaluate : 5.509 ------------------------------------------------------------------------------- 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 42 THR Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain B residue 38 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 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 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 29 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 129 ILE 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 499 MET Chi-restraints excluded: chain g residue 22 VAL 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 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 489 ASP Chi-restraints excluded: chain G residue 497 GLU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 80 VAL 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 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 492 VAL 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 95 GLN 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 480 LEU Chi-restraints excluded: chain q residue 114 LEU Chi-restraints excluded: chain q residue 406 LYS Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 67 MET 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 112 GLU Chi-restraints excluded: chain Z residue 132 GLN Chi-restraints excluded: chain Z residue 136 GLU Chi-restraints excluded: chain Z residue 459 LEU 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 61 ASN Chi-restraints excluded: chain z residue 408 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 131 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 270 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 342 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 154 optimal weight: 0.0670 chunk 213 optimal weight: 2.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 482 ASN ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** b 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** D 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 GLN E 467 ASN E 493 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 420 HIS ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.125790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110798 restraints weight = 77319.011| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.37 r_work: 0.3573 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.7579 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= 0.126 Angle : 0.649 17.565 46321 Z= 0.317 Chirality : 0.041 0.219 5617 Planarity : 0.004 0.079 5931 Dihedral : 4.736 98.495 4773 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.77 % Allowed : 21.84 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.13), residues: 4407 helix: 1.95 (0.09), residues: 2900 sheet: -0.33 (0.35), residues: 199 loop : -1.07 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 435 HIS 0.010 0.001 HIS b 391 PHE 0.013 0.001 PHE h 381 TYR 0.022 0.001 TYR q 505 ARG 0.010 0.000 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 2162) hydrogen bonds : angle 3.77072 ( 6366) covalent geometry : bond 0.00286 (34273) covalent geometry : angle 0.64861 (46321) Misc. bond : bond 0.00073 ( 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 878 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 777 time to evaluate : 3.712 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: 0.9034 (mt0) cc_final: 0.8334 (mp10) REVERT: a 95 ILE cc_start: 0.9366 (pt) cc_final: 0.9046 (mt) REVERT: a 99 GLU cc_start: 0.8367 (tp30) cc_final: 0.8003 (tp30) REVERT: a 106 GLU cc_start: 0.8090 (tp30) cc_final: 0.7708 (tp30) REVERT: a 443 ARG cc_start: 0.8994 (mtm110) cc_final: 0.8755 (ttp80) REVERT: a 529 ASP cc_start: 0.8158 (p0) cc_final: 0.7787 (p0) REVERT: A 51 ASP cc_start: 0.7526 (m-30) cc_final: 0.7289 (m-30) REVERT: A 105 ASP cc_start: 0.8633 (t70) cc_final: 0.8404 (t0) REVERT: A 109 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8501 (mmtp) REVERT: A 424 GLU cc_start: 0.8767 (tt0) cc_final: 0.8466 (tt0) REVERT: A 434 GLU cc_start: 0.8689 (mp0) cc_final: 0.7934 (mp0) REVERT: A 440 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 443 ARG cc_start: 0.8655 (mtp-110) cc_final: 0.8097 (ttp-110) REVERT: A 473 GLU cc_start: 0.8579 (tp30) cc_final: 0.8147 (tp30) REVERT: b 48 MET cc_start: 0.8745 (mmm) cc_final: 0.8338 (mmp) REVERT: b 49 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7702 (t0) REVERT: b 53 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7286 (pp) REVERT: b 82 LYS cc_start: 0.9115 (ttmt) cc_final: 0.8549 (tptp) REVERT: b 97 ASP cc_start: 0.5542 (t0) cc_final: 0.4997 (m-30) REVERT: b 111 ARG cc_start: 0.9287 (OUTLIER) cc_final: 0.8273 (ptp-110) REVERT: b 120 LYS cc_start: 0.9485 (mtmt) cc_final: 0.9144 (mmtm) REVERT: b 426 ASN cc_start: 0.8333 (m-40) cc_final: 0.7934 (m-40) REVERT: b 441 LYS cc_start: 0.8892 (mptt) cc_final: 0.8426 (mptt) REVERT: b 453 ASN cc_start: 0.8946 (m-40) cc_final: 0.8713 (m-40) REVERT: b 460 ASP cc_start: 0.8610 (t0) cc_final: 0.8351 (t0) REVERT: B 66 ASP cc_start: 0.8198 (t0) cc_final: 0.7968 (t70) REVERT: B 73 ASN cc_start: 0.8249 (p0) cc_final: 0.8048 (p0) REVERT: B 91 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7521 (tp40) REVERT: B 438 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.9063 (p) REVERT: B 502 GLN cc_start: 0.8899 (tp40) cc_final: 0.8663 (tp40) REVERT: D 32 GLN cc_start: 0.8602 (pt0) cc_final: 0.8265 (pt0) REVERT: D 57 MET cc_start: 0.8923 (mmm) cc_final: 0.8662 (mmt) REVERT: D 80 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8100 (mp10) REVERT: D 472 ASN cc_start: 0.8494 (t0) cc_final: 0.8268 (t0) REVERT: d 49 ARG cc_start: 0.8902 (ptm-80) cc_final: 0.8576 (ttp80) REVERT: d 81 MET cc_start: 0.8351 (mmm) cc_final: 0.7995 (mmm) REVERT: d 481 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8537 (ttp-170) REVERT: E 30 GLU cc_start: 0.8173 (pm20) cc_final: 0.7831 (pm20) REVERT: E 82 ASP cc_start: 0.7358 (m-30) cc_final: 0.7150 (m-30) REVERT: E 144 GLU cc_start: 0.8359 (pt0) cc_final: 0.8139 (pp20) REVERT: E 442 GLU cc_start: 0.7654 (mp0) cc_final: 0.7289 (mp0) REVERT: E 447 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7379 (mtt180) REVERT: E 454 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8053 (mt-10) REVERT: E 470 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7764 (tm-30) REVERT: E 524 MET cc_start: 0.8990 (tpp) cc_final: 0.8552 (tpp) REVERT: e 46 MET cc_start: 0.9097 (mmp) cc_final: 0.8727 (mmm) REVERT: e 442 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: g 38 ARG cc_start: 0.8900 (mmm-85) cc_final: 0.8415 (ttp80) REVERT: g 47 MET cc_start: 0.8785 (mmm) cc_final: 0.8511 (mmm) REVERT: g 69 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7921 (mm-30) REVERT: g 71 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7949 (mp10) REVERT: g 511 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8266 (tm-30) REVERT: G 20 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6586 (ttp80) REVERT: G 38 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.7583 (tmm-80) REVERT: G 47 MET cc_start: 0.9007 (mmm) cc_final: 0.8354 (mmm) REVERT: G 54 MET cc_start: 0.7935 (mpp) cc_final: 0.7677 (mpp) REVERT: G 59 MET cc_start: 0.8325 (mmt) cc_final: 0.7746 (mmt) REVERT: G 68 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8725 (mpp80) REVERT: G 87 GLN cc_start: 0.8615 (tm-30) cc_final: 0.7908 (tm-30) REVERT: G 415 GLU cc_start: 0.8458 (mp0) cc_final: 0.8186 (mp0) REVERT: G 489 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7493 (t70) REVERT: h 61 ASP cc_start: 0.8337 (t70) cc_final: 0.8010 (t70) REVERT: h 67 LYS cc_start: 0.8616 (mttm) cc_final: 0.8415 (mmtp) REVERT: h 105 LEU cc_start: 0.9399 (mt) cc_final: 0.9074 (mt) REVERT: h 184 MET cc_start: 0.3894 (mtp) cc_final: 0.3642 (mtm) REVERT: h 387 ARG cc_start: 0.7295 (ptm-80) cc_final: 0.6946 (ptm160) REVERT: h 394 MET cc_start: 0.8189 (mmp) cc_final: 0.7908 (mmp) REVERT: h 497 MET cc_start: 0.8693 (mmm) cc_final: 0.8488 (mmm) REVERT: h 508 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8296 (mp0) REVERT: h 511 CYS cc_start: 0.8813 (m) cc_final: 0.8585 (m) REVERT: H 99 LEU cc_start: 0.9266 (mp) cc_final: 0.8993 (mp) REVERT: H 419 TYR cc_start: 0.8775 (t80) cc_final: 0.8457 (t80) REVERT: H 455 PHE cc_start: 0.8408 (m-80) cc_final: 0.8156 (m-80) REVERT: H 521 LYS cc_start: 0.8334 (ttpp) cc_final: 0.7765 (tmtt) REVERT: Q 14 MET cc_start: 0.4562 (ppp) cc_final: 0.4047 (mtm) REVERT: Q 38 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8296 (pt0) REVERT: Q 41 GLN cc_start: 0.8778 (tp40) cc_final: 0.8399 (tp40) REVERT: Q 79 GLN cc_start: 0.8624 (mp10) cc_final: 0.8284 (mp10) REVERT: Q 116 GLU cc_start: 0.7628 (tp30) cc_final: 0.6731 (tp30) REVERT: Q 120 ARG cc_start: 0.8690 (mpt-90) cc_final: 0.7825 (mmt180) REVERT: q 34 GLN cc_start: 0.8080 (tp40) cc_final: 0.7740 (mm110) REVERT: q 41 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8237 (tp-100) REVERT: q 55 MET cc_start: 0.8758 (mtm) cc_final: 0.8208 (mtm) REVERT: q 74 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8436 (tmm-80) REVERT: q 133 GLU cc_start: 0.8351 (mp0) cc_final: 0.8128 (mp0) REVERT: q 385 MET cc_start: 0.4486 (mtt) cc_final: 0.3447 (ttt) REVERT: Z 59 ASP cc_start: 0.8374 (t0) cc_final: 0.7897 (p0) REVERT: Z 442 ASP cc_start: 0.8357 (m-30) cc_final: 0.8001 (m-30) REVERT: Z 453 GLN cc_start: 0.9212 (mt0) cc_final: 0.8980 (mt0) REVERT: Z 462 THR cc_start: 0.9351 (m) cc_final: 0.9017 (t) REVERT: Z 487 MET cc_start: 0.8691 (tmm) cc_final: 0.8400 (ppp) REVERT: Z 520 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7543 (tm-30) REVERT: z 23 ASN cc_start: 0.8506 (m110) cc_final: 0.8008 (m-40) REVERT: z 46 MET cc_start: 0.8356 (ttm) cc_final: 0.8059 (ttm) REVERT: z 404 ASP cc_start: 0.8136 (t0) cc_final: 0.7828 (t0) outliers start: 101 outliers final: 74 residues processed: 842 average time/residue: 0.4932 time to fit residues: 664.2358 Evaluate side-chains 796 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 712 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 499 LYS 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 505 GLU Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain B residue 38 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 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 84 LEU 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 29 LEU Chi-restraints excluded: chain E residue 441 LEU Chi-restraints excluded: chain E residue 461 SER Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 129 ILE 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 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 422 LEU 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 22 VAL Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 58 VAL Chi-restraints excluded: chain G residue 117 MET Chi-restraints excluded: chain G residue 489 ASP Chi-restraints excluded: chain G residue 497 GLU 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 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 492 VAL 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 95 GLN 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 114 LEU Chi-restraints excluded: chain q residue 406 LYS Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 110 ILE Chi-restraints excluded: chain Z residue 112 GLU Chi-restraints excluded: chain Z residue 132 GLN 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 61 ASN Chi-restraints excluded: chain z residue 384 LEU Chi-restraints excluded: chain z residue 408 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 377 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 349 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 397 optimal weight: 0.9990 chunk 282 optimal weight: 0.0370 chunk 332 optimal weight: 4.9990 chunk 348 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN E 493 HIS ** e 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 21 GLN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 459 ASN H 30 GLN H 448 GLN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 380 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.126916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.111960 restraints weight = 76293.531| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.39 r_work: 0.3582 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.7666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34276 Z= 0.125 Angle : 0.665 18.040 46321 Z= 0.325 Chirality : 0.042 0.230 5617 Planarity : 0.004 0.087 5931 Dihedral : 4.728 98.969 4773 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.72 % Allowed : 22.23 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.13), residues: 4407 helix: 1.96 (0.09), residues: 2896 sheet: -0.26 (0.36), residues: 199 loop : -1.01 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 435 HIS 0.011 0.001 HIS b 391 PHE 0.012 0.001 PHE h 381 TYR 0.021 0.001 TYR H 423 ARG 0.011 0.000 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 2162) hydrogen bonds : angle 3.76477 ( 6366) covalent geometry : bond 0.00286 (34273) covalent geometry : angle 0.66544 (46321) Misc. bond : bond 0.00071 ( 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 864 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 765 time to evaluate : 3.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 17 ILE cc_start: 0.8181 (mm) cc_final: 0.7554 (mm) REVERT: a 20 GLN cc_start: 0.9046 (mt0) cc_final: 0.8339 (mp10) REVERT: a 95 ILE cc_start: 0.9377 (pt) cc_final: 0.9065 (mt) REVERT: a 99 GLU cc_start: 0.8394 (tp30) cc_final: 0.8020 (tp30) REVERT: a 106 GLU cc_start: 0.8065 (tp30) cc_final: 0.7697 (tp30) REVERT: a 443 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8751 (ttp80) REVERT: A 51 ASP cc_start: 0.7664 (m-30) cc_final: 0.7372 (m-30) REVERT: A 105 ASP cc_start: 0.8626 (t70) cc_final: 0.8368 (t0) REVERT: A 109 LYS cc_start: 0.8820 (mmtp) cc_final: 0.8370 (mmtp) REVERT: A 110 GLN cc_start: 0.8424 (mm-40) cc_final: 0.8143 (mp10) REVERT: A 424 GLU cc_start: 0.8795 (tt0) cc_final: 0.8494 (tt0) REVERT: A 434 GLU cc_start: 0.8656 (mp0) cc_final: 0.7970 (mp0) REVERT: A 440 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8005 (mm-30) REVERT: A 443 ARG cc_start: 0.8693 (mtp-110) cc_final: 0.8186 (ttp-110) REVERT: A 473 GLU cc_start: 0.8680 (tp30) cc_final: 0.8289 (tp30) REVERT: b 49 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7707 (t0) REVERT: b 53 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7253 (pp) REVERT: b 82 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8548 (tptp) REVERT: b 97 ASP cc_start: 0.5588 (t0) cc_final: 0.4951 (m-30) REVERT: b 111 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8209 (ptp-110) REVERT: b 120 LYS cc_start: 0.9427 (mtmt) cc_final: 0.9109 (mmtm) REVERT: b 426 ASN cc_start: 0.8403 (m-40) cc_final: 0.7995 (m-40) REVERT: b 437 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7692 (tm-30) REVERT: b 441 LYS cc_start: 0.8904 (mptt) cc_final: 0.8489 (mptt) REVERT: b 453 ASN cc_start: 0.8926 (m-40) cc_final: 0.8707 (m-40) REVERT: b 460 ASP cc_start: 0.8623 (t0) cc_final: 0.8327 (t0) REVERT: B 66 ASP cc_start: 0.8401 (t0) cc_final: 0.8165 (t70) REVERT: B 73 ASN cc_start: 0.8279 (p0) cc_final: 0.8033 (p0) REVERT: B 91 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7547 (tp40) REVERT: B 438 SER cc_start: 0.9421 (OUTLIER) cc_final: 0.9074 (p) REVERT: B 522 LYS cc_start: 0.8384 (mttt) cc_final: 0.7976 (ptpp) REVERT: D 32 GLN cc_start: 0.8533 (pt0) cc_final: 0.8204 (pt0) REVERT: D 57 MET cc_start: 0.8926 (mmm) cc_final: 0.8662 (mmt) REVERT: D 80 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: D 151 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5841 (mmm) REVERT: D 472 ASN cc_start: 0.8504 (t0) cc_final: 0.8268 (t0) REVERT: d 49 ARG cc_start: 0.8882 (ptm-80) cc_final: 0.8565 (ttp80) REVERT: d 81 MET cc_start: 0.8414 (mmm) cc_final: 0.7996 (mmm) REVERT: d 150 ASP cc_start: 0.7597 (p0) cc_final: 0.7331 (m-30) REVERT: d 446 MET cc_start: 0.8566 (mtm) cc_final: 0.8170 (mtt) REVERT: d 481 ARG cc_start: 0.8903 (ttp-170) cc_final: 0.8595 (ttp-170) REVERT: E 71 ASP cc_start: 0.7432 (p0) cc_final: 0.7205 (m-30) REVERT: E 119 GLU cc_start: 0.8825 (tt0) cc_final: 0.8602 (tp30) REVERT: E 442 GLU cc_start: 0.7852 (mp0) cc_final: 0.7485 (mp0) REVERT: E 454 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8149 (mt-10) REVERT: E 470 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7769 (tm-30) REVERT: E 524 MET cc_start: 0.9046 (tpp) cc_final: 0.8598 (tpp) REVERT: e 44 ASN cc_start: 0.8383 (m-40) cc_final: 0.8144 (m110) REVERT: e 46 MET cc_start: 0.9058 (mmp) cc_final: 0.8716 (mmm) REVERT: g 38 ARG cc_start: 0.8907 (mmm-85) cc_final: 0.8413 (ttp80) REVERT: g 47 MET cc_start: 0.8854 (mmm) cc_final: 0.8627 (mmm) REVERT: g 69 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7943 (mm-30) REVERT: g 71 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7942 (mp10) REVERT: g 503 LEU cc_start: 0.9145 (mt) cc_final: 0.8943 (mp) REVERT: g 511 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8300 (tm-30) REVERT: G 20 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6383 (ttp80) REVERT: G 38 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7481 (tmm-80) REVERT: G 47 MET cc_start: 0.9027 (mmm) cc_final: 0.8302 (mmm) REVERT: G 54 MET cc_start: 0.7681 (mpp) cc_final: 0.7479 (mpp) REVERT: G 59 MET cc_start: 0.8304 (mmt) cc_final: 0.7730 (mmt) REVERT: G 68 ARG cc_start: 0.8958 (tpp80) cc_final: 0.8671 (mpp80) REVERT: G 415 GLU cc_start: 0.8541 (mp0) cc_final: 0.8223 (mp0) REVERT: G 461 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8298 (mtt90) REVERT: G 489 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7496 (t70) REVERT: h 61 ASP cc_start: 0.8375 (t70) cc_final: 0.8011 (t70) REVERT: h 67 LYS cc_start: 0.8630 (mttm) cc_final: 0.8427 (mmtp) REVERT: h 105 LEU cc_start: 0.9386 (mt) cc_final: 0.9071 (mt) REVERT: h 170 GLN cc_start: 0.5714 (tm-30) cc_final: 0.5410 (tm-30) REVERT: h 184 MET cc_start: 0.3951 (mtp) cc_final: 0.3736 (mtt) REVERT: h 387 ARG cc_start: 0.7351 (ptm-80) cc_final: 0.7014 (ptm160) REVERT: h 394 MET cc_start: 0.8176 (mmp) cc_final: 0.7904 (mmp) REVERT: h 443 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8281 (pt0) REVERT: h 508 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: h 511 CYS cc_start: 0.8835 (m) cc_final: 0.8597 (m) REVERT: H 99 LEU cc_start: 0.9265 (mp) cc_final: 0.8978 (mp) REVERT: H 103 GLU cc_start: 0.8500 (tp30) cc_final: 0.7923 (tp30) REVERT: H 106 LYS cc_start: 0.8774 (tttt) cc_final: 0.8199 (ttpt) REVERT: H 419 TYR cc_start: 0.8753 (t80) cc_final: 0.8394 (t80) REVERT: H 455 PHE cc_start: 0.8417 (m-80) cc_final: 0.8160 (m-80) REVERT: H 521 LYS cc_start: 0.8389 (ttpp) cc_final: 0.7893 (tmtt) REVERT: Q 14 MET cc_start: 0.4567 (ppp) cc_final: 0.4045 (mtm) REVERT: Q 38 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8308 (pt0) REVERT: Q 41 GLN cc_start: 0.8746 (tp40) cc_final: 0.8232 (tp-100) REVERT: Q 79 GLN cc_start: 0.8592 (mp10) cc_final: 0.8240 (mp10) REVERT: Q 116 GLU cc_start: 0.7586 (tp30) cc_final: 0.6852 (tp30) REVERT: Q 137 ARG cc_start: 0.8666 (ptp-110) cc_final: 0.8454 (mtm110) REVERT: q 34 GLN cc_start: 0.8113 (tp40) cc_final: 0.7694 (mm110) REVERT: q 41 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8240 (tp-100) REVERT: q 74 ARG cc_start: 0.8853 (ttp80) cc_final: 0.8481 (tmm-80) REVERT: q 130 GLU cc_start: 0.8214 (pt0) cc_final: 0.7431 (mt-10) REVERT: q 133 GLU cc_start: 0.8536 (mp0) cc_final: 0.8225 (mp0) REVERT: q 385 MET cc_start: 0.4537 (mtt) cc_final: 0.3582 (ttt) REVERT: Z 59 ASP cc_start: 0.8296 (t0) cc_final: 0.7892 (p0) REVERT: Z 442 ASP cc_start: 0.8353 (m-30) cc_final: 0.7985 (m-30) REVERT: Z 453 GLN cc_start: 0.9272 (mt0) cc_final: 0.9036 (mt0) REVERT: Z 462 THR cc_start: 0.9099 (m) cc_final: 0.8748 (t) REVERT: Z 487 MET cc_start: 0.8676 (tmm) cc_final: 0.8396 (ppp) REVERT: Z 520 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7537 (tm-30) outliers start: 99 outliers final: 70 residues processed: 831 average time/residue: 0.4894 time to fit residues: 646.4517 Evaluate side-chains 805 residues out of total 3640 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 723 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 443 ARG Chi-restraints excluded: chain a residue 499 LYS 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 505 GLU Chi-restraints excluded: chain b residue 49 ASP Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 111 ARG Chi-restraints excluded: chain b residue 389 SER Chi-restraints excluded: chain b residue 434 VAL Chi-restraints excluded: chain b residue 446 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 151 MET Chi-restraints excluded: chain D residue 446 MET 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 461 SER Chi-restraints excluded: chain E residue 505 ILE Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 122 LEU Chi-restraints excluded: chain e residue 129 ILE 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 59 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 107 SER Chi-restraints excluded: chain g residue 422 LEU 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 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 489 ASP Chi-restraints excluded: chain G residue 497 GLU 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 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 492 VAL 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 95 GLN Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 114 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 114 LEU Chi-restraints excluded: chain q residue 406 LYS Chi-restraints excluded: chain q residue 463 VAL Chi-restraints excluded: chain q residue 497 ILE Chi-restraints excluded: chain Z residue 47 LEU Chi-restraints excluded: chain Z residue 94 SER Chi-restraints excluded: chain Z residue 112 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 34 LEU Chi-restraints excluded: chain z residue 61 ASN Chi-restraints excluded: chain z residue 408 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 38 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 301 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 312 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 391 HIS B 91 GLN D 468 ASN ** d 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 HIS h 21 GLN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 380 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.126899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.111830 restraints weight = 76439.702| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.33 r_work: 0.3596 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.7797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34276 Z= 0.125 Angle : 0.668 17.647 46321 Z= 0.327 Chirality : 0.041 0.226 5617 Planarity : 0.004 0.080 5931 Dihedral : 4.709 99.700 4773 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.47 % Allowed : 22.91 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.13), residues: 4407 helix: 1.98 (0.09), residues: 2902 sheet: -0.17 (0.37), residues: 189 loop : -1.00 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 435 HIS 0.010 0.001 HIS b 391 PHE 0.008 0.001 PHE H 455 TYR 0.021 0.001 TYR q 505 ARG 0.011 0.001 ARG a 18 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 2162) hydrogen bonds : angle 3.74287 ( 6366) covalent geometry : bond 0.00285 (34273) covalent geometry : angle 0.66845 (46321) Misc. bond : bond 0.00069 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21612.83 seconds wall clock time: 378 minutes 3.92 seconds (22683.92 seconds total)