Starting phenix.real_space_refine on Fri Sep 27 19:40:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/09_2024/7wu7_32823.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/09_2024/7wu7_32823.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/09_2024/7wu7_32823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/09_2024/7wu7_32823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/09_2024/7wu7_32823.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wu7_32823/09_2024/7wu7_32823.cif" } resolution = 3.85 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= 0.019 sd= 0.246 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 416 5.16 5 C 42020 2.51 5 N 11626 2.21 5 O 12961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 67031 Number of models: 1 Model: "" Number of chains: 26 Chain: "1" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 873 Classifications: {'peptide': 107} Link IDs: {'TRANS': 106} Chain: "2" Number of atoms: 667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 667 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "3" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 956 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 3, 'TRANS': 112} Chain: "4" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 711 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "5" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1017 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "6" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 825 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "A" Number of atoms: 3919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3919 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 12, 'TRANS': 503} Chain: "B" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3736 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 8, 'TRANS': 488} Chain: "C" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3924 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 16, 'TRANS': 488} Chain: "D" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3847 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 496} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3883 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "F" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "G" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3910 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain: "H" Number of atoms: 3816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3816 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 12, 'TRANS': 487} Chain: "I" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 3903 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 12, 'TRANS': 501} Chain: "J" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 497, 3736 Classifications: {'peptide': 497} Link IDs: {'PTRANS': 8, 'TRANS': 488} Chain: "K" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3924 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 16, 'TRANS': 488} Chain: "L" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3847 Classifications: {'peptide': 511} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 496} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3883 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain: "N" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "O" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 3910 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain: "P" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3830 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 12, 'TRANS': 489} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" 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: 31.64, per 1000 atoms: 0.47 Number of scatterers: 67031 At special positions: 0 Unit cell: (230.52, 176.46, 185.64, 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 416 16.00 P 8 15.00 O 12961 8.00 N 11626 7.00 C 42020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.21 Conformation dependent library (CDL) restraints added in 7.0 seconds 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16330 Finding SS restraints... Secondary structure from input PDB file: 333 helices and 96 sheets defined 57.8% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.21 Creating SS restraints... Processing helix chain '1' and resid 13 through 55 removed outlier: 3.929A pdb=" N ILE 1 32 " --> pdb=" O LYS 1 28 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU 1 37 " --> pdb=" O GLN 1 33 " (cutoff:3.500A) Processing helix chain '1' and resid 72 through 83 removed outlier: 3.618A pdb=" N LEU 1 81 " --> pdb=" O HIS 1 77 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS 1 83 " --> pdb=" O GLN 1 79 " (cutoff:3.500A) Processing helix chain '1' and resid 83 through 111 removed outlier: 4.123A pdb=" N TYR 1 100 " --> pdb=" O GLN 1 96 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA 1 108 " --> pdb=" O SER 1 104 " (cutoff:3.500A) Processing helix chain '1' and resid 112 through 117 removed outlier: 4.092A pdb=" N MET 1 117 " --> pdb=" O ARG 1 113 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 57 removed outlier: 4.261A pdb=" N GLU 2 36 " --> pdb=" O ARG 2 32 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA 2 44 " --> pdb=" O LEU 2 40 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU 2 47 " --> pdb=" O LYS 2 43 " (cutoff:3.500A) Processing helix chain '2' and resid 58 through 63 Processing helix chain '2' and resid 85 through 108 removed outlier: 3.649A pdb=" N ASN 2 93 " --> pdb=" O ALA 2 89 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS 2 94 " --> pdb=" O LEU 2 90 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN 2 96 " --> pdb=" O ASN 2 92 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS 2 99 " --> pdb=" O GLU 2 95 " (cutoff:3.500A) Processing helix chain '3' and resid 55 through 91 removed outlier: 3.998A pdb=" N LYS 3 70 " --> pdb=" O ASN 3 66 " (cutoff:3.500A) Proline residue: 3 79 - end of helix removed outlier: 3.940A pdb=" N LEU 3 88 " --> pdb=" O THR 3 84 " (cutoff:3.500A) Processing helix chain '3' and resid 91 through 99 removed outlier: 4.553A pdb=" N SER 3 97 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) Processing helix chain '3' and resid 138 through 167 removed outlier: 3.549A pdb=" N ALA 3 142 " --> pdb=" O ASP 3 138 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS 3 146 " --> pdb=" O ALA 3 142 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN 3 147 " --> pdb=" O LEU 3 143 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU 3 148 " --> pdb=" O LEU 3 144 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA 3 151 " --> pdb=" O ASN 3 147 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS 3 153 " --> pdb=" O SER 3 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN 3 154 " --> pdb=" O THR 3 150 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU 3 162 " --> pdb=" O LEU 3 158 " (cutoff:3.500A) Processing helix chain '4' and resid 28 through 60 removed outlier: 5.182A pdb=" N GLU 4 35 " --> pdb=" O SER 4 31 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU 4 36 " --> pdb=" O ARG 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 83 through 113 removed outlier: 4.209A pdb=" N GLU 4 89 " --> pdb=" O GLU 4 85 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU 4 97 " --> pdb=" O ASN 4 93 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU 4 112 " --> pdb=" O ILE 4 108 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 40 removed outlier: 3.755A pdb=" N ASN 5 20 " --> pdb=" O GLU 5 16 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN 5 21 " --> pdb=" O MET 5 17 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN 5 40 " --> pdb=" O LEU 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 40 through 56 removed outlier: 4.512A pdb=" N ASN 5 51 " --> pdb=" O LYS 5 47 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL 5 52 " --> pdb=" O ASP 5 48 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU 5 53 " --> pdb=" O CYS 5 49 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN 5 54 " --> pdb=" O LEU 5 50 " (cutoff:3.500A) Processing helix chain '5' and resid 78 through 81 Processing helix chain '5' and resid 95 through 101 Processing helix chain '5' and resid 102 through 135 Proline residue: 5 119 - end of helix removed outlier: 4.414A pdb=" N LYS 5 124 " --> pdb=" O ALA 5 120 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET 5 127 " --> pdb=" O GLU 5 123 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS 5 128 " --> pdb=" O LYS 5 124 " (cutoff:3.500A) Processing helix chain '6' and resid 14 through 48 removed outlier: 3.829A pdb=" N GLY 6 29 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU 6 39 " --> pdb=" O ALA 6 35 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE 6 42 " --> pdb=" O THR 6 38 " (cutoff:3.500A) Processing helix chain '6' and resid 68 through 114 removed outlier: 3.956A pdb=" N ALA 6 72 " --> pdb=" O GLU 6 68 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU 6 102 " --> pdb=" O GLU 6 98 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN 6 103 " --> pdb=" O ARG 6 99 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG 6 105 " --> pdb=" O SER 6 101 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU 6 108 " --> pdb=" O GLN 6 104 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA 6 109 " --> pdb=" O ARG 6 105 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU 6 111 " --> pdb=" O THR 6 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 34 removed outlier: 3.748A pdb=" N ALA A 24 " --> pdb=" O GLN A 20 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.623A pdb=" N ILE A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 110 Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.900A pdb=" N ASN A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.711A pdb=" N GLY A 186 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN A 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 183 through 187' Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.652A pdb=" N VAL A 195 " --> pdb=" O VAL A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 282 removed outlier: 5.415A pdb=" N ARG A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.532A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 326 through 330 removed outlier: 4.379A pdb=" N THR A 330 " --> pdb=" O ILE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 381 through 405 removed outlier: 4.326A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 428 removed outlier: 3.816A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 removed outlier: 4.163A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 455 Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.584A pdb=" N LEU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 484 Processing helix chain 'A' and resid 507 through 524 Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.586A pdb=" N ILE B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.651A pdb=" N LEU B 43 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 72 removed outlier: 3.705A pdb=" N ILE B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.678A pdb=" N VAL B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 152 through 169 Processing helix chain 'B' and resid 175 through 191 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.659A pdb=" N ASP B 247 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 3.791A pdb=" N HIS B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 286 removed outlier: 3.722A pdb=" N MET B 275 " --> pdb=" O GLU B 271 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N VAL B 279 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 318 No H-bonds generated for 'chain 'B' and resid 316 through 318' Processing helix chain 'B' and resid 319 through 328 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 379 through 402 Processing helix chain 'B' and resid 411 through 428 Processing helix chain 'B' and resid 431 through 455 removed outlier: 3.714A pdb=" N ALA B 435 " --> pdb=" O LYS B 431 " (cutoff:3.500A) removed outlier: 3.665A 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 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'C' and resid 20 through 39 removed outlier: 4.586A pdb=" N THR C 39 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.722A pdb=" N ILE C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 91 removed outlier: 3.734A pdb=" N GLU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 114 removed outlier: 3.620A pdb=" N HIS C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 141 Processing helix chain 'C' and resid 148 through 161 removed outlier: 3.574A pdb=" N MET C 152 " --> pdb=" O ASP C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 168 through 181 removed outlier: 4.475A pdb=" N ASN C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.595A pdb=" N ASP C 211 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 212 " --> pdb=" O ILE C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 262 through 281 removed outlier: 3.924A pdb=" N ARG C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 269 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP C 281 " --> pdb=" O GLN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 285 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.516A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 327 removed outlier: 3.876A pdb=" N ASN C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 404 removed outlier: 3.615A pdb=" N SER C 385 " --> pdb=" O LYS C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 428 removed outlier: 4.060A pdb=" N ALA C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 445 removed outlier: 4.118A pdb=" N ALA C 441 " --> pdb=" O TYR C 437 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN C 442 " --> pdb=" O ARG C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 455 Processing helix chain 'C' and resid 460 through 471 Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'C' and resid 498 through 518 removed outlier: 3.670A pdb=" N LYS C 502 " --> pdb=" O PRO C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 50 removed outlier: 4.573A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 127 removed outlier: 3.659A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 Processing helix chain 'D' and resid 179 through 195 Proline residue: D 185 - end of helix removed outlier: 3.920A pdb=" N ILE D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 294 removed outlier: 4.361A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 removed outlier: 3.597A pdb=" N LYS D 319 " --> pdb=" O HIS D 315 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 339 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 444 through 459 removed outlier: 3.963A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 467 removed outlier: 3.554A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 511 through 531 removed outlier: 4.189A pdb=" N SER D 515 " --> pdb=" O PRO D 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 50 removed outlier: 3.721A pdb=" N ALA E 33 " --> pdb=" O MET E 29 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'E' and resid 85 through 98 removed outlier: 3.727A pdb=" N GLN E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 126 removed outlier: 4.540A pdb=" N GLY E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 149 Processing helix chain 'E' and resid 161 through 176 removed outlier: 4.384A pdb=" N THR E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR E 172 " --> pdb=" O THR E 168 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.916A pdb=" N ALA E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA E 197 " --> pdb=" O VAL E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 295 removed outlier: 4.019A pdb=" N MET E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 removed outlier: 3.945A pdb=" N LEU E 313 " --> pdb=" O GLU E 309 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 437 Processing helix chain 'E' and resid 438 through 440 No H-bonds generated for 'chain 'E' and resid 438 through 440' Processing helix chain 'E' and resid 443 through 456 removed outlier: 3.762A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 465 Processing helix chain 'E' and resid 469 through 484 removed outlier: 3.709A pdb=" N VAL E 482 " --> pdb=" O ARG E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 505 removed outlier: 3.881A pdb=" N GLN E 504 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 529 removed outlier: 3.911A pdb=" N ILE E 527 " --> pdb=" O MET E 523 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 36 removed outlier: 4.476A pdb=" N THR F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 67 Processing helix chain 'F' and resid 72 through 87 removed outlier: 4.132A pdb=" N ILE F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 111 removed outlier: 3.774A pdb=" N TYR F 109 " --> pdb=" O GLN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 138 removed outlier: 3.712A pdb=" N ILE F 119 " --> pdb=" O HIS F 115 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU F 136 " --> pdb=" O GLN F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 157 Processing helix chain 'F' and resid 161 through 180 removed outlier: 4.268A pdb=" N GLU F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 183 No H-bonds generated for 'chain 'F' and resid 181 through 183' Processing helix chain 'F' and resid 252 through 260 removed outlier: 3.868A pdb=" N ARG F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 283 removed outlier: 4.071A pdb=" N ILE F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU F 268 " --> pdb=" O ARG F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 308 removed outlier: 3.586A pdb=" N LEU F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA F 304 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS F 307 " --> pdb=" O ASP F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 329 removed outlier: 3.966A pdb=" N MET F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU F 322 " --> pdb=" O ARG F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 404 removed outlier: 3.712A pdb=" N GLN F 386 " --> pdb=" O HIS F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 426 Processing helix chain 'F' and resid 430 through 432 No H-bonds generated for 'chain 'F' and resid 430 through 432' Processing helix chain 'F' and resid 433 through 456 removed outlier: 4.199A pdb=" N ILE F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) Proline residue: F 448 - end of helix Processing helix chain 'F' and resid 458 through 474 removed outlier: 3.532A pdb=" N THR F 462 " --> pdb=" O ASP F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 493 Processing helix chain 'F' and resid 498 through 518 Processing helix chain 'G' and resid 18 through 35 removed outlier: 3.601A pdb=" N SER G 24 " --> pdb=" O PRO G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 40 removed outlier: 4.271A pdb=" N LEU G 40 " --> pdb=" O ARG G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 73 through 90 Processing helix chain 'G' and resid 92 through 115 removed outlier: 4.343A pdb=" N SER G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 117 through 140 removed outlier: 3.979A pdb=" N ILE G 121 " --> pdb=" O HIS G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 164 Processing helix chain 'G' and resid 170 through 185 Processing helix chain 'G' and resid 222 through 227 removed outlier: 3.958A pdb=" N GLU G 226 " --> pdb=" O TYR G 222 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 222 through 227' Processing helix chain 'G' and resid 263 through 284 removed outlier: 3.512A pdb=" N VAL G 267 " --> pdb=" O TYR G 263 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP G 271 " --> pdb=" O VAL G 267 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE G 273 " --> pdb=" O ALA G 269 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 306 Processing helix chain 'G' and resid 315 through 325 removed outlier: 3.565A pdb=" N LEU G 319 " --> pdb=" O PRO G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 402 removed outlier: 3.666A pdb=" N GLU G 383 " --> pdb=" O GLU G 379 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU G 384 " --> pdb=" O GLN G 380 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG G 397 " --> pdb=" O ILE G 393 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS G 401 " --> pdb=" O ARG G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 410 through 425 removed outlier: 3.663A pdb=" N MET G 414 " --> pdb=" O GLY G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 430 through 442 removed outlier: 3.851A pdb=" N LEU G 434 " --> pdb=" O LYS G 430 " (cutoff:3.500A) Processing helix chain 'G' and resid 443 through 455 Processing helix chain 'G' and resid 456 through 471 removed outlier: 3.966A pdb=" N LYS G 463 " --> pdb=" O ASN G 459 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY G 471 " --> pdb=" O ARG G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 515 Processing helix chain 'H' and resid 28 through 45 removed outlier: 3.803A pdb=" N ALA H 35 " --> pdb=" O ARG H 31 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N CYS H 36 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR H 45 " --> pdb=" O GLN H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 76 Processing helix chain 'H' and resid 80 through 97 Processing helix chain 'H' and resid 100 through 122 removed outlier: 3.665A pdb=" N LEU H 105 " --> pdb=" O THR H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 143 Processing helix chain 'H' and resid 144 through 147 Processing helix chain 'H' and resid 156 through 172 removed outlier: 3.826A pdb=" N SER H 162 " --> pdb=" O ASP H 158 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR H 166 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER H 167 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 188 removed outlier: 3.738A pdb=" N LEU H 179 " --> pdb=" O ASN H 175 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA H 180 " --> pdb=" O GLU H 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 262 through 283 removed outlier: 3.578A pdb=" N PHE H 268 " --> pdb=" O GLU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 309 Processing helix chain 'H' and resid 317 through 329 Processing helix chain 'H' and resid 340 through 344 removed outlier: 3.570A pdb=" N GLU H 343 " --> pdb=" O VAL H 340 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET H 344 " --> pdb=" O LEU H 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 340 through 344' Processing helix chain 'H' and resid 381 through 405 removed outlier: 3.802A pdb=" N ASP H 387 " --> pdb=" O ASN H 383 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 430 Processing helix chain 'H' and resid 434 through 457 removed outlier: 3.822A pdb=" N ILE H 448 " --> pdb=" O ALA H 444 " (cutoff:3.500A) Proline residue: H 449 - end of helix Processing helix chain 'H' and resid 459 through 472 Processing helix chain 'H' and resid 501 through 520 Processing helix chain 'I' and resid 17 through 34 removed outlier: 3.570A pdb=" N VAL I 32 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER I 34 " --> pdb=" O ASN I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 65 Processing helix chain 'I' and resid 69 through 87 Processing helix chain 'I' and resid 89 through 110 Processing helix chain 'I' and resid 113 through 135 Processing helix chain 'I' and resid 141 through 144 Processing helix chain 'I' and resid 145 through 158 removed outlier: 4.369A pdb=" N ALA I 151 " --> pdb=" O CYS I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 178 removed outlier: 3.849A pdb=" N ALA I 169 " --> pdb=" O GLY I 165 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP I 174 " --> pdb=" O ASN I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 191 through 193 No H-bonds generated for 'chain 'I' and resid 191 through 193' Processing helix chain 'I' and resid 225 through 229 removed outlier: 3.846A pdb=" N ARG I 228 " --> pdb=" O MET I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 261 through 282 removed outlier: 4.113A pdb=" N THR I 281 " --> pdb=" O LYS I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 304 removed outlier: 3.636A pdb=" N VAL I 301 " --> pdb=" O LEU I 297 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLU I 302 " --> pdb=" O LYS I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 322 Processing helix chain 'I' and resid 326 through 330 Processing helix chain 'I' and resid 341 through 343 No H-bonds generated for 'chain 'I' and resid 341 through 343' Processing helix chain 'I' and resid 355 through 359 removed outlier: 3.646A pdb=" N ASP I 358 " --> pdb=" O ARG I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 405 Processing helix chain 'I' and resid 413 through 429 Processing helix chain 'I' and resid 434 through 445 removed outlier: 3.668A pdb=" N ALA I 439 " --> pdb=" O GLN I 435 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 456 Processing helix chain 'I' and resid 459 through 477 removed outlier: 3.787A pdb=" N ALA I 465 " --> pdb=" O THR I 461 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN I 477 " --> pdb=" O GLU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 484 removed outlier: 3.612A pdb=" N LYS I 481 " --> pdb=" O PRO I 478 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN I 482 " --> pdb=" O GLU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 526 Processing helix chain 'J' and resid 29 through 41 removed outlier: 3.655A pdb=" N GLY J 36 " --> pdb=" O ALA J 32 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N SER J 41 " --> pdb=" O ASP J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 58 removed outlier: 4.084A pdb=" N ASP J 58 " --> pdb=" O SER J 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 55 through 58' Processing helix chain 'J' and resid 66 through 74 removed outlier: 3.568A pdb=" N ILE J 70 " --> pdb=" O ASP J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 90 Processing helix chain 'J' and resid 98 through 119 removed outlier: 3.996A pdb=" N VAL J 104 " --> pdb=" O THR J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 145 Processing helix chain 'J' and resid 151 through 167 Processing helix chain 'J' and resid 172 through 189 removed outlier: 3.805A pdb=" N ARG J 189 " --> pdb=" O GLU J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 260 through 267 removed outlier: 3.612A pdb=" N VAL J 264 " --> pdb=" O THR J 261 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ALA J 265 " --> pdb=" O ALA J 262 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE J 267 " --> pdb=" O VAL J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 286 removed outlier: 3.987A pdb=" N LYS J 272 " --> pdb=" O GLU J 268 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU J 273 " --> pdb=" O HIS J 269 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS J 278 " --> pdb=" O LYS J 274 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG J 281 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 308 Processing helix chain 'J' and resid 316 through 328 Processing helix chain 'J' and resid 337 through 341 Processing helix chain 'J' and resid 379 through 403 removed outlier: 3.636A pdb=" N GLU J 385 " --> pdb=" O GLN J 381 " (cutoff:3.500A) Processing helix chain 'J' and resid 411 through 428 removed outlier: 3.714A pdb=" N ARG J 427 " --> pdb=" O GLN J 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 431 through 454 removed outlier: 4.151A pdb=" N ALA J 435 " --> pdb=" O LYS J 431 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU J 446 " --> pdb=" O ALA J 442 " (cutoff:3.500A) Proline residue: J 447 - end of helix Processing helix chain 'J' and resid 457 through 469 Processing helix chain 'J' and resid 488 through 492 removed outlier: 3.510A pdb=" N GLY J 492 " --> pdb=" O MET J 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 488 through 492' Processing helix chain 'J' and resid 497 through 517 removed outlier: 3.810A pdb=" N VAL J 517 " --> pdb=" O VAL J 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 38 Processing helix chain 'K' and resid 62 through 70 removed outlier: 3.628A pdb=" N ILE K 66 " --> pdb=" O ASP K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 removed outlier: 4.142A pdb=" N MET K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 114 removed outlier: 3.859A pdb=" N ILE K 100 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS K 111 " --> pdb=" O SER K 107 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE K 112 " --> pdb=" O VAL K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 141 removed outlier: 3.635A pdb=" N SER K 141 " --> pdb=" O LEU K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 164 removed outlier: 3.961A pdb=" N MET K 152 " --> pdb=" O ASP K 148 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASN K 154 " --> pdb=" O ASP K 150 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA K 164 " --> pdb=" O ILE K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 184 removed outlier: 3.971A pdb=" N ASN K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 175 " --> pdb=" O LEU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 208 through 212 Processing helix chain 'K' and resid 246 through 250 removed outlier: 3.849A pdb=" N LYS K 249 " --> pdb=" O GLU K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 286 removed outlier: 3.806A pdb=" N GLU K 271 " --> pdb=" O ILE K 267 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN K 284 " --> pdb=" O GLU K 280 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU K 285 " --> pdb=" O ASP K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 302 Processing helix chain 'K' and resid 316 through 328 removed outlier: 4.143A pdb=" N ALA K 324 " --> pdb=" O ASN K 320 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 404 removed outlier: 4.081A pdb=" N LEU K 384 " --> pdb=" O SER K 380 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL K 387 " --> pdb=" O ILE K 383 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU K 388 " --> pdb=" O LEU K 384 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG K 389 " --> pdb=" O SER K 385 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP K 393 " --> pdb=" O ARG K 389 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU K 403 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 428 removed outlier: 4.258A pdb=" N MET K 416 " --> pdb=" O GLY K 412 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA K 417 " --> pdb=" O ALA K 413 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA K 428 " --> pdb=" O GLU K 424 " (cutoff:3.500A) Processing helix chain 'K' and resid 433 through 444 Processing helix chain 'K' and resid 445 through 456 Processing helix chain 'K' and resid 458 through 472 Processing helix chain 'K' and resid 499 through 518 Processing helix chain 'L' and resid 29 through 50 removed outlier: 4.499A pdb=" N THR L 50 " --> pdb=" O ASP L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 79 removed outlier: 3.750A pdb=" N LEU L 78 " --> pdb=" O GLY L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 103 Processing helix chain 'L' and resid 105 through 127 removed outlier: 4.062A pdb=" N VAL L 110 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 152 removed outlier: 3.515A pdb=" N SER L 152 " --> pdb=" O LEU L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 173 removed outlier: 4.023A pdb=" N SER L 173 " --> pdb=" O THR L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 195 removed outlier: 5.419A pdb=" N LEU L 182 " --> pdb=" O GLN L 178 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU L 183 " --> pdb=" O TYR L 179 " (cutoff:3.500A) Proline residue: L 185 - end of helix Processing helix chain 'L' and resid 271 through 292 removed outlier: 3.888A pdb=" N VAL L 275 " --> pdb=" O GLN L 271 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU L 284 " --> pdb=" O ARG L 280 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS L 292 " --> pdb=" O LYS L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 320 removed outlier: 4.778A pdb=" N PHE L 316 " --> pdb=" O LEU L 312 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET L 320 " --> pdb=" O PHE L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 329 through 341 Processing helix chain 'L' and resid 347 through 351 removed outlier: 3.854A pdb=" N GLN L 350 " --> pdb=" O HIS L 347 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 354 No H-bonds generated for 'chain 'L' and resid 352 through 354' Processing helix chain 'L' and resid 394 through 417 Processing helix chain 'L' and resid 426 through 443 Processing helix chain 'L' and resid 446 through 459 removed outlier: 3.947A pdb=" N CYS L 450 " --> pdb=" O MET L 446 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU L 459 " --> pdb=" O ALA L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 459 through 470 Processing helix chain 'L' and resid 472 through 485 Processing helix chain 'L' and resid 511 through 532 removed outlier: 3.922A pdb=" N SER L 515 " --> pdb=" O PRO L 511 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 49 removed outlier: 3.660A pdb=" N ALA M 33 " --> pdb=" O MET M 29 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 81 removed outlier: 4.114A pdb=" N MET M 80 " --> pdb=" O THR M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 97 removed outlier: 3.800A pdb=" N LYS M 89 " --> pdb=" O HIS M 85 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 103 removed outlier: 3.569A pdb=" N GLY M 103 " --> pdb=" O ASP M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 126 removed outlier: 3.617A pdb=" N GLN M 122 " --> pdb=" O GLU M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 149 Processing helix chain 'M' and resid 162 through 174 Processing helix chain 'M' and resid 182 through 195 removed outlier: 4.677A pdb=" N ALA M 186 " --> pdb=" O HIS M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 296 removed outlier: 3.656A pdb=" N THR M 295 " --> pdb=" O GLN M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 317 Processing helix chain 'M' and resid 326 through 337 removed outlier: 4.136A pdb=" N GLU M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 348 Processing helix chain 'M' and resid 391 through 415 Processing helix chain 'M' and resid 423 through 438 removed outlier: 4.230A pdb=" N ASP M 438 " --> pdb=" O SER M 434 " (cutoff:3.500A) Processing helix chain 'M' and resid 443 through 466 removed outlier: 3.839A pdb=" N ILE M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) Proline residue: M 459 - end of helix removed outlier: 3.650A pdb=" N SER M 466 " --> pdb=" O LEU M 462 " (cutoff:3.500A) Processing helix chain 'M' and resid 469 through 484 Processing helix chain 'M' and resid 500 through 505 Processing helix chain 'M' and resid 509 through 530 Processing helix chain 'N' and resid 19 through 35 removed outlier: 4.080A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 64 Processing helix chain 'N' and resid 71 through 86 Processing helix chain 'N' and resid 91 through 111 removed outlier: 3.633A pdb=" N ASN N 95 " --> pdb=" O GLY N 91 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL N 96 " --> pdb=" O THR N 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 138 removed outlier: 3.814A pdb=" N ILE N 119 " --> pdb=" O HIS N 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN N 132 " --> pdb=" O GLU N 128 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 136 " --> pdb=" O GLN N 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 144 through 157 Processing helix chain 'N' and resid 161 through 178 removed outlier: 4.466A pdb=" N ASP N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL N 167 " --> pdb=" O GLU N 163 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU N 168 " --> pdb=" O LEU N 164 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA N 171 " --> pdb=" O VAL N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 255 Processing helix chain 'N' and resid 256 through 283 removed outlier: 3.533A pdb=" N VAL N 260 " --> pdb=" O ARG N 256 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU N 263 " --> pdb=" O LEU N 259 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ARG N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL N 271 " --> pdb=" O ILE N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 298 through 306 removed outlier: 3.895A pdb=" N LEU N 302 " --> pdb=" O ASP N 298 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER N 306 " --> pdb=" O LEU N 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 329 removed outlier: 3.619A pdb=" N MET N 321 " --> pdb=" O LYS N 317 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY N 329 " --> pdb=" O THR N 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 381 through 404 removed outlier: 3.825A pdb=" N ASP N 404 " --> pdb=" O ASN N 400 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 426 Processing helix chain 'N' and resid 427 through 429 No H-bonds generated for 'chain 'N' and resid 427 through 429' Processing helix chain 'N' and resid 430 through 431 No H-bonds generated for 'chain 'N' and resid 430 through 431' Processing helix chain 'N' and resid 432 through 445 Processing helix chain 'N' and resid 445 through 455 Processing helix chain 'N' and resid 459 through 473 removed outlier: 3.552A pdb=" N LEU N 463 " --> pdb=" O LEU N 459 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL N 464 " --> pdb=" O GLN N 460 " (cutoff:3.500A) Processing helix chain 'N' and resid 489 through 493 Processing helix chain 'N' and resid 498 through 517 Processing helix chain 'O' and resid 18 through 38 removed outlier: 3.627A pdb=" N ALA O 35 " --> pdb=" O VAL O 31 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL O 36 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 69 Processing helix chain 'O' and resid 73 through 86 removed outlier: 3.744A pdb=" N GLN O 86 " --> pdb=" O ILE O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 114 removed outlier: 3.948A pdb=" N SER O 96 " --> pdb=" O ASP O 92 " (cutoff:3.500A) Proline residue: O 110 - end of helix Processing helix chain 'O' and resid 119 through 140 Processing helix chain 'O' and resid 148 through 150 No H-bonds generated for 'chain 'O' and resid 148 through 150' Processing helix chain 'O' and resid 151 through 163 removed outlier: 4.298A pdb=" N LYS O 157 " --> pdb=" O LYS O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 170 through 186 removed outlier: 3.918A pdb=" N PHE O 174 " --> pdb=" O GLN O 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 196 removed outlier: 3.732A pdb=" N ILE O 195 " --> pdb=" O LEU O 192 " (cutoff:3.500A) Processing helix chain 'O' and resid 256 through 260 removed outlier: 4.196A pdb=" N THR O 259 " --> pdb=" O ARG O 256 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL O 260 " --> pdb=" O VAL O 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 260' Processing helix chain 'O' and resid 261 through 284 removed outlier: 3.908A pdb=" N ILE O 266 " --> pdb=" O ASP O 262 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL O 267 " --> pdb=" O TYR O 263 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU O 270 " --> pdb=" O ILE O 266 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 306 Processing helix chain 'O' and resid 315 through 327 Processing helix chain 'O' and resid 379 through 402 removed outlier: 4.344A pdb=" N ARG O 387 " --> pdb=" O GLU O 383 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N HIS O 390 " --> pdb=" O GLU O 386 " (cutoff:3.500A) Processing helix chain 'O' and resid 410 through 427 removed outlier: 3.904A pdb=" N ARG O 421 " --> pdb=" O SER O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 430 through 442 removed outlier: 4.045A pdb=" N LEU O 434 " --> pdb=" O LYS O 430 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 453 Processing helix chain 'O' and resid 456 through 468 removed outlier: 3.906A pdb=" N ILE O 460 " --> pdb=" O ASP O 456 " (cutoff:3.500A) Processing helix chain 'O' and resid 496 through 515 Processing helix chain 'P' and resid 28 through 45 removed outlier: 3.827A pdb=" N THR P 45 " --> pdb=" O GLN P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 76 Processing helix chain 'P' and resid 80 through 97 Processing helix chain 'P' and resid 100 through 122 removed outlier: 3.812A pdb=" N LEU P 105 " --> pdb=" O THR P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 147 Proline residue: P 144 - end of helix Processing helix chain 'P' and resid 156 through 172 removed outlier: 3.551A pdb=" N VAL P 160 " --> pdb=" O ASP P 156 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N THR P 166 " --> pdb=" O SER P 162 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N SER P 167 " --> pdb=" O LEU P 163 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS P 171 " --> pdb=" O SER P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 191 removed outlier: 3.647A pdb=" N ILE P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 211 through 215 removed outlier: 3.638A pdb=" N SER P 214 " --> pdb=" O GLY P 211 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 282 Processing helix chain 'P' and resid 282 through 287 removed outlier: 3.919A pdb=" N THR P 286 " --> pdb=" O ALA P 282 " (cutoff:3.500A) Processing helix chain 'P' and resid 298 through 308 Processing helix chain 'P' and resid 317 through 327 Processing helix chain 'P' and resid 340 through 344 Processing helix chain 'P' and resid 354 through 358 Processing helix chain 'P' and resid 381 through 405 Processing helix chain 'P' and resid 413 through 430 Processing helix chain 'P' and resid 434 through 457 removed outlier: 3.858A pdb=" N ILE P 448 " --> pdb=" O ALA P 444 " (cutoff:3.500A) Proline residue: P 449 - end of helix Processing helix chain 'P' and resid 459 through 472 Processing helix chain 'P' and resid 492 through 496 Processing helix chain 'P' and resid 501 through 520 Processing sheet with id=AA1, first strand: chain '2' and resid 69 through 73 removed outlier: 3.839A pdb=" N LEU 1 70 " --> pdb=" O GLU 5 61 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU 5 61 " --> pdb=" O LEU 1 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL 5 64 " --> pdb=" O VAL 5 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL 5 72 " --> pdb=" O VAL 5 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 69 through 73 removed outlier: 3.839A pdb=" N LEU 1 70 " --> pdb=" O GLU 5 61 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU 5 61 " --> pdb=" O LEU 1 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL 5 64 " --> pdb=" O VAL 5 72 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL 5 72 " --> pdb=" O VAL 5 64 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU 3 133 " --> pdb=" O LEU 3 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '4' and resid 69 through 70 Processing sheet with id=AA4, first strand: chain '5' and resid 82 through 86 removed outlier: 3.544A pdb=" N VAL 5 86 " --> pdb=" O TYR 5 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '6' and resid 57 through 58 Processing sheet with id=AA6, first strand: chain 'A' and resid 53 through 55 removed outlier: 7.253A pdb=" N ASP A 42 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N ILE C 522 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N MET A 44 " --> pdb=" O ILE C 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA8, first strand: chain 'A' and resid 196 through 200 removed outlier: 6.218A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 306 through 311 removed outlier: 3.871A pdb=" N ARG A 310 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 233 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU A 287 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA A 235 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR A 289 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE A 234 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.919A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 488 Processing sheet with id=AB3, first strand: chain 'A' and resid 527 through 531 removed outlier: 3.950A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 62 through 64 Processing sheet with id=AB5, first strand: chain 'B' and resid 199 through 205 removed outlier: 4.330A pdb=" N LEU B 375 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 204 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 220 Processing sheet with id=AB7, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.922A pdb=" N ILE B 239 " --> pdb=" O GLU B 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 406 through 407 Processing sheet with id=AB9, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.947A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 517 through 521 removed outlier: 4.185A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 57 through 60 removed outlier: 3.848A pdb=" N THR C 60 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 213 through 215 removed outlier: 3.903A pdb=" N CYS C 213 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AC5, first strand: chain 'C' and resid 239 through 241 removed outlier: 3.778A pdb=" N VAL C 239 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL C 290 " --> pdb=" O ILE C 312 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 478 through 481 removed outlier: 3.703A pdb=" N THR C 486 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 210 through 213 removed outlier: 6.290A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 227 through 230 removed outlier: 3.573A pdb=" N LEU D 373 " --> pdb=" O VAL D 365 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 365 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.758A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 210 through 215 removed outlier: 3.567A pdb=" N LYS E 214 " --> pdb=" O ILE E 387 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 227 through 229 removed outlier: 3.563A pdb=" N GLU E 375 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU E 358 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 321 through 322 removed outlier: 8.087A pdb=" N VAL E 322 " --> pdb=" O ASN E 298 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS E 247 " --> pdb=" O ALA E 297 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N LEU E 299 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 418 through 420 Processing sheet with id=AD5, first strand: chain 'F' and resid 54 through 57 removed outlier: 3.854A pdb=" N LYS F 45 " --> pdb=" O THR F 57 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N MET F 44 " --> pdb=" O ASP H 522 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE H 524 " --> pdb=" O MET F 44 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET F 46 " --> pdb=" O ILE H 524 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 192 through 195 removed outlier: 7.160A pdb=" N GLU F 192 " --> pdb=" O LEU F 374 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE F 376 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET F 194 " --> pdb=" O ILE F 376 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 210 through 212 removed outlier: 4.003A pdb=" N GLU F 358 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU F 355 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS F 366 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA F 347 " --> pdb=" O CYS F 366 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL F 225 " --> pdb=" O VAL F 350 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 210 through 212 removed outlier: 4.003A pdb=" N GLU F 358 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU F 355 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N CYS F 366 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA F 347 " --> pdb=" O CYS F 366 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N TYR F 229 " --> pdb=" O VAL F 290 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ILE F 292 " --> pdb=" O TYR F 229 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N LEU F 231 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 407 through 409 Processing sheet with id=AE1, first strand: chain 'F' and resid 478 through 479 Processing sheet with id=AE2, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.823A pdb=" N LYS G 47 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 197 through 200 removed outlier: 6.269A pdb=" N LYS G 198 " --> pdb=" O LEU G 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'G' and resid 310 through 311 removed outlier: 6.186A pdb=" N LYS G 236 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU G 290 " --> pdb=" O LYS G 236 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA G 238 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY G 343 " --> pdb=" O ILE G 237 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 347 through 353 removed outlier: 3.808A pdb=" N TYR G 358 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 405 through 407 Processing sheet with id=AE7, first strand: chain 'G' and resid 476 through 478 removed outlier: 3.795A pdb=" N ASP G 483 " --> pdb=" O ASP G 478 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 516 through 520 removed outlier: 6.448A pdb=" N ASN H 53 " --> pdb=" O VAL G 516 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU G 518 " --> pdb=" O ASN H 53 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET H 55 " --> pdb=" O GLU G 518 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE H 64 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 149 through 150 removed outlier: 4.151A pdb=" N CYS H 149 " --> pdb=" O LEU H 408 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 202 through 208 removed outlier: 6.580A pdb=" N ARG H 203 " --> pdb=" O ILE H 375 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LEU H 377 " --> pdb=" O ARG H 203 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N CYS H 205 " --> pdb=" O LEU H 377 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY H 379 " --> pdb=" O CYS H 205 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE H 207 " --> pdb=" O GLY H 379 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 221 through 223 Processing sheet with id=AF3, first strand: chain 'H' and resid 227 through 228 removed outlier: 7.352A pdb=" N VAL H 291 " --> pdb=" O VAL H 313 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 479 through 480 Processing sheet with id=AF5, first strand: chain 'I' and resid 43 through 48 removed outlier: 3.804A pdb=" N THR I 55 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU I 45 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR I 53 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASP I 47 " --> pdb=" O ASP I 51 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ASP I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 195 through 198 removed outlier: 6.145A pdb=" N ASN I 196 " --> pdb=" O ILE I 375 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 214 through 216 removed outlier: 3.758A pdb=" N LEU I 361 " --> pdb=" O GLU I 354 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU I 354 " --> pdb=" O LEU I 361 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 234 through 235 Processing sheet with id=AF9, first strand: chain 'I' and resid 237 through 239 removed outlier: 6.853A pdb=" N LEU I 237 " --> pdb=" O LEU I 287 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'I' and resid 408 through 410 Processing sheet with id=AG2, first strand: chain 'I' and resid 486 through 487 removed outlier: 3.543A pdb=" N ARG I 496 " --> pdb=" O GLY I 487 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 527 through 529 Processing sheet with id=AG4, first strand: chain 'J' and resid 61 through 64 removed outlier: 6.209A pdb=" N ILE J 51 " --> pdb=" O VAL L 536 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 146 through 147 Processing sheet with id=AG6, first strand: chain 'J' and resid 200 through 202 removed outlier: 6.233A pdb=" N HIS J 200 " --> pdb=" O ILE J 373 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU J 375 " --> pdb=" O HIS J 200 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE J 202 " --> pdb=" O LEU J 375 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR J 372 " --> pdb=" O ASP J 215 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 232 through 235 removed outlier: 6.862A pdb=" N LYS J 347 " --> pdb=" O ASN J 234 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU J 359 " --> pdb=" O VAL J 352 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 238 through 239 removed outlier: 6.961A pdb=" N LEU J 238 " --> pdb=" O ILE J 291 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE J 290 " --> pdb=" O ILE J 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'J' and resid 476 through 479 Processing sheet with id=AH1, first strand: chain 'J' and resid 520 through 522 removed outlier: 4.151A pdb=" N ILE J 521 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL M 62 " --> pdb=" O ILE J 521 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.578A pdb=" N VAL K 58 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET N 522 " --> pdb=" O MET K 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 142 through 143 Processing sheet with id=AH4, first strand: chain 'K' and resid 217 through 224 removed outlier: 4.289A pdb=" N THR K 361 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS K 222 " --> pdb=" O TYR K 359 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N TYR K 359 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE K 360 " --> pdb=" O LYS K 353 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=AH6, first strand: chain 'K' and resid 289 through 291 removed outlier: 6.382A pdb=" N VAL K 290 " --> pdb=" O ILE K 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'L' and resid 210 through 212 Processing sheet with id=AH8, first strand: chain 'L' and resid 227 through 231 removed outlier: 3.556A pdb=" N LEU L 227 " --> pdb=" O ILE L 376 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 245 through 247 Processing sheet with id=AI1, first strand: chain 'L' and resid 297 through 299 removed outlier: 6.324A pdb=" N LEU L 298 " --> pdb=" O ILE L 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'L' and resid 422 through 423 Processing sheet with id=AI3, first strand: chain 'L' and resid 492 through 494 removed outlier: 3.514A pdb=" N GLY L 499 " --> pdb=" O ASN L 494 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'M' and resid 211 through 213 removed outlier: 3.644A pdb=" N ILE M 387 " --> pdb=" O GLU M 212 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 227 through 230 Processing sheet with id=AI6, first strand: chain 'M' and resid 248 through 250 Processing sheet with id=AI7, first strand: chain 'N' and resid 56 through 57 removed outlier: 7.148A pdb=" N MET N 44 " --> pdb=" O VAL P 521 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N GLN P 523 " --> pdb=" O MET N 44 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET N 46 " --> pdb=" O GLN P 523 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'N' and resid 139 through 140 Processing sheet with id=AI9, first strand: chain 'N' and resid 191 through 197 removed outlier: 3.938A pdb=" N MET N 196 " --> pdb=" O ILE N 376 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY N 378 " --> pdb=" O MET N 196 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'N' and resid 210 through 211 Processing sheet with id=AJ2, first strand: chain 'N' and resid 311 through 313 removed outlier: 6.922A pdb=" N VAL N 291 " --> pdb=" O LEU N 313 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR N 229 " --> pdb=" O VAL N 290 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE N 292 " --> pdb=" O TYR N 229 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU N 231 " --> pdb=" O ILE N 292 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'N' and resid 477 through 479 Processing sheet with id=AJ4, first strand: chain 'O' and resid 47 through 49 Processing sheet with id=AJ5, first strand: chain 'O' and resid 198 through 199 removed outlier: 3.619A pdb=" N LEU O 374 " --> pdb=" O LYS O 198 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 214 through 216 removed outlier: 3.916A pdb=" N ASN O 359 " --> pdb=" O PHE O 216 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL O 347 " --> pdb=" O THR O 362 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'O' and resid 236 through 240 removed outlier: 6.157A pdb=" N LYS O 236 " --> pdb=" O ALA O 286 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL O 288 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS O 287 " --> pdb=" O PHE O 309 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA O 311 " --> pdb=" O LYS O 287 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL O 289 " --> pdb=" O ALA O 311 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'O' and resid 405 through 407 Processing sheet with id=AJ9, first strand: chain 'O' and resid 475 through 477 Processing sheet with id=AK1, first strand: chain 'O' and resid 516 through 521 removed outlier: 4.464A pdb=" N MET P 55 " --> pdb=" O ASP O 517 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N THR O 519 " --> pdb=" O MET P 55 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE P 57 " --> pdb=" O THR O 519 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS O 521 " --> pdb=" O ILE P 57 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE P 64 " --> pdb=" O VAL P 56 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'P' and resid 149 through 150 removed outlier: 4.181A pdb=" N CYS P 149 " --> pdb=" O LEU P 408 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P' and resid 202 through 205 removed outlier: 6.218A pdb=" N ARG P 203 " --> pdb=" O ILE P 375 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER P 216 " --> pdb=" O VAL P 376 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'P' and resid 221 through 222 Processing sheet with id=AK5, first strand: chain 'P' and resid 312 through 313 removed outlier: 4.058A pdb=" N VAL P 313 " --> pdb=" O VAL P 291 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE P 239 " --> pdb=" O GLY P 345 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY P 345 " --> pdb=" O ILE P 239 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'P' and resid 478 through 480 3820 hydrogen bonds defined for protein. 11091 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: 30.04 Time building geometry restraints manager: 15.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 17799 1.33 - 1.45: 10055 1.45 - 1.58: 39214 1.58 - 1.70: 21 1.70 - 1.82: 690 Bond restraints: 67779 Sorted by residual: bond pdb=" C4' ADP N 601 " pdb=" O4' ADP N 601 " ideal model delta sigma weight residual 1.426 1.619 -0.193 2.00e-02 2.50e+03 9.26e+01 bond pdb=" C4' ADP P 601 " pdb=" O4' ADP P 601 " ideal model delta sigma weight residual 1.426 1.615 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" C4' ADP F 601 " pdb=" O4' ADP F 601 " ideal model delta sigma weight residual 1.426 1.614 -0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" C3' ADP P 601 " pdb=" C4' ADP P 601 " ideal model delta sigma weight residual 1.524 1.338 0.186 2.00e-02 2.50e+03 8.60e+01 bond pdb=" C3' ADP H5000 " pdb=" C4' ADP H5000 " ideal model delta sigma weight residual 1.524 1.339 0.185 2.00e-02 2.50e+03 8.60e+01 ... (remaining 67774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 89565 2.41 - 4.82: 1541 4.82 - 7.23: 257 7.23 - 9.64: 55 9.64 - 12.05: 23 Bond angle restraints: 91441 Sorted by residual: angle pdb=" N THR N 92 " pdb=" CA THR N 92 " pdb=" C THR N 92 " ideal model delta sigma weight residual 111.28 123.21 -11.93 1.09e+00 8.42e-01 1.20e+02 angle pdb=" N VAL I 39 " pdb=" CA VAL I 39 " pdb=" C VAL I 39 " ideal model delta sigma weight residual 112.29 107.51 4.78 9.40e-01 1.13e+00 2.59e+01 angle pdb=" N GLU 1 95 " pdb=" CA GLU 1 95 " pdb=" CB GLU 1 95 " ideal model delta sigma weight residual 110.12 116.96 -6.84 1.47e+00 4.63e-01 2.16e+01 angle pdb=" N ASP 4 62 " pdb=" CA ASP 4 62 " pdb=" C ASP 4 62 " ideal model delta sigma weight residual 113.21 108.25 4.96 1.15e+00 7.56e-01 1.86e+01 angle pdb=" N LEU O 186 " pdb=" CA LEU O 186 " pdb=" C LEU O 186 " ideal model delta sigma weight residual 110.80 101.73 9.07 2.13e+00 2.20e-01 1.81e+01 ... (remaining 91436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.63: 41164 32.63 - 65.27: 824 65.27 - 97.90: 117 97.90 - 130.53: 3 130.53 - 163.17: 3 Dihedral angle restraints: 42111 sinusoidal: 16932 harmonic: 25179 Sorted by residual: dihedral pdb=" O1B ADP H5000 " pdb=" O3A ADP H5000 " pdb=" PB ADP H5000 " pdb=" PA ADP H5000 " ideal model delta sinusoidal sigma weight residual -60.00 103.16 -163.17 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP H5000 " pdb=" O5' ADP H5000 " pdb=" PA ADP H5000 " pdb=" O2A ADP H5000 " ideal model delta sinusoidal sigma weight residual -60.00 103.01 -163.01 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" O1B ADP F 601 " pdb=" O3A ADP F 601 " pdb=" PB ADP F 601 " pdb=" PA ADP F 601 " ideal model delta sinusoidal sigma weight residual -60.00 76.80 -136.80 1 2.00e+01 2.50e-03 4.15e+01 ... (remaining 42108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 10108 0.086 - 0.172: 820 0.172 - 0.258: 23 0.258 - 0.344: 2 0.344 - 0.429: 2 Chirality restraints: 10955 Sorted by residual: chirality pdb=" CA THR N 92 " pdb=" N THR N 92 " pdb=" C THR N 92 " pdb=" CB THR N 92 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CB ILE G 195 " pdb=" CA ILE G 195 " pdb=" CG1 ILE G 195 " pdb=" CG2 ILE G 195 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB ILE D 461 " pdb=" CA ILE D 461 " pdb=" CG1 ILE D 461 " pdb=" CG2 ILE D 461 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 10952 not shown) Planarity restraints: 11721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY N 89 " -0.020 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C GLY N 89 " 0.072 2.00e-02 2.50e+03 pdb=" O GLY N 89 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP N 90 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG O 397 " -0.014 2.00e-02 2.50e+03 2.84e-02 8.04e+00 pdb=" C ARG O 397 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG O 397 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG O 398 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 165 " 0.241 9.50e-02 1.11e+02 1.08e-01 7.52e+00 pdb=" NE ARG P 165 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG P 165 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG P 165 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG P 165 " 0.012 2.00e-02 2.50e+03 ... (remaining 11718 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1836 2.70 - 3.25: 74974 3.25 - 3.80: 109267 3.80 - 4.35: 142877 4.35 - 4.90: 226414 Nonbonded interactions: 555368 Sorted by model distance: nonbonded pdb=" O ASP M 198 " pdb=" OD1 ASP M 198 " model vdw 2.146 3.040 nonbonded pdb=" OG SER D 501 " pdb=" OE2 GLU D 506 " model vdw 2.199 3.040 nonbonded pdb=" O THR I 154 " pdb=" OG SER I 158 " model vdw 2.199 3.040 nonbonded pdb=" OG SER H 170 " pdb=" O1A ADP H5000 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR 3 152 " pdb=" OD2 ASP 3 156 " model vdw 2.201 3.040 ... (remaining 555363 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' and resid 16 through 529) selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = (chain 'D' and (resid 28 through 502 or (resid 503 and (name N or name CA or nam \ e C or name O or name CB )) or resid 504 through 538)) selection = (chain 'L' and (resid 28 through 501 or (resid 502 through 503 and (name N or na \ me CA or name C or name O or name CB )) or resid 504 through 538)) } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = (chain 'P' and (resid 27 through 526 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.060 Extract box with map and model: 2.220 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 125.240 Find NCS groups from input model: 4.770 Set up NCS constraints: 0.420 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 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 : 0.005 0.193 67779 Z= 0.297 Angle : 0.808 12.049 91441 Z= 0.411 Chirality : 0.047 0.429 10955 Planarity : 0.005 0.108 11721 Dihedral : 14.101 163.166 25781 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 0.01 % Allowed : 0.30 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.14 (0.09), residues: 8683 helix: 0.18 (0.08), residues: 4470 sheet: -1.78 (0.21), residues: 556 loop : -1.74 (0.10), residues: 3657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 485 HIS 0.013 0.001 HIS C 470 PHE 0.044 0.002 PHE J 179 TYR 0.036 0.002 TYR O 302 ARG 0.016 0.001 ARG K 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1630 time to evaluate : 5.901 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: 1 117 MET cc_start: 0.6107 (mmp) cc_final: 0.5391 (mmp) REVERT: 3 123 VAL cc_start: 0.6317 (p) cc_final: 0.6086 (m) REVERT: 5 78 ASP cc_start: 0.6304 (m-30) cc_final: 0.5997 (m-30) REVERT: 5 117 ILE cc_start: 0.6324 (mm) cc_final: 0.6049 (mm) REVERT: A 111 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8031 (mmmt) REVERT: C 40 CYS cc_start: 0.8228 (m) cc_final: 0.7982 (m) REVERT: C 110 GLU cc_start: 0.8224 (tp30) cc_final: 0.7889 (pt0) REVERT: C 188 ASN cc_start: 0.6350 (t0) cc_final: 0.5967 (t0) REVERT: C 438 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7048 (ttm170) REVERT: C 473 GLU cc_start: 0.8883 (mp0) cc_final: 0.8555 (pm20) REVERT: C 476 GLU cc_start: 0.7224 (mp0) cc_final: 0.6850 (mp0) REVERT: C 499 LEU cc_start: 0.8325 (tp) cc_final: 0.7977 (tp) REVERT: D 33 ILE cc_start: 0.8204 (mm) cc_final: 0.7958 (mm) REVERT: D 268 ASP cc_start: 0.7381 (m-30) cc_final: 0.7181 (m-30) REVERT: D 405 ILE cc_start: 0.8586 (pt) cc_final: 0.8333 (tp) REVERT: D 532 ILE cc_start: 0.8576 (mm) cc_final: 0.8200 (mt) REVERT: E 436 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7658 (tm-30) REVERT: E 446 TYR cc_start: 0.7936 (m-80) cc_final: 0.7381 (m-80) REVERT: E 503 GLN cc_start: 0.7729 (mp-120) cc_final: 0.7510 (mp10) REVERT: E 504 GLN cc_start: 0.8610 (tp40) cc_final: 0.8322 (tp-100) REVERT: F 36 THR cc_start: 0.8255 (p) cc_final: 0.7601 (t) REVERT: F 67 MET cc_start: 0.7774 (mtp) cc_final: 0.7232 (mtm) REVERT: F 143 MET cc_start: 0.5122 (mmp) cc_final: 0.4833 (mtt) REVERT: F 381 LYS cc_start: 0.8546 (mmmt) cc_final: 0.8074 (mmmm) REVERT: F 522 MET cc_start: 0.6869 (mmp) cc_final: 0.6346 (mmp) REVERT: G 32 ILE cc_start: 0.9089 (tp) cc_final: 0.8887 (tp) REVERT: H 387 ASP cc_start: 0.8067 (t0) cc_final: 0.7833 (t0) REVERT: H 404 ARG cc_start: 0.8215 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: I 99 GLU cc_start: 0.7039 (tp30) cc_final: 0.6186 (tp30) REVERT: I 102 LYS cc_start: 0.7832 (tmmt) cc_final: 0.7593 (ttpt) REVERT: I 134 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6804 (mt-10) REVERT: I 209 MET cc_start: 0.7113 (mmm) cc_final: 0.6902 (mmp) REVERT: I 432 SER cc_start: 0.7269 (p) cc_final: 0.6358 (p) REVERT: K 305 MET cc_start: 0.7674 (mmm) cc_final: 0.7460 (mmp) REVERT: K 396 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6552 (mm-40) REVERT: L 60 MET cc_start: 0.6603 (pmm) cc_final: 0.6252 (pmm) REVERT: L 112 ILE cc_start: 0.8996 (mm) cc_final: 0.8781 (mt) REVERT: L 355 MET cc_start: 0.5068 (ppp) cc_final: 0.4798 (ppp) REVERT: M 119 GLU cc_start: 0.7759 (tp30) cc_final: 0.7380 (tp30) REVERT: M 239 MET cc_start: -0.1279 (ppp) cc_final: -0.1509 (ppp) REVERT: M 288 MET cc_start: 0.4005 (mtm) cc_final: 0.3709 (mmm) REVERT: M 485 MET cc_start: 0.7597 (mmm) cc_final: 0.7283 (mmp) REVERT: M 505 HIS cc_start: 0.5924 (t70) cc_final: 0.5443 (t70) REVERT: N 66 GLU cc_start: 0.7507 (pt0) cc_final: 0.7113 (pt0) REVERT: N 461 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7405 (tm-30) REVERT: O 65 ILE cc_start: 0.8709 (pt) cc_final: 0.8494 (pt) REVERT: O 396 VAL cc_start: 0.8755 (m) cc_final: 0.8452 (p) REVERT: P 344 MET cc_start: 0.4119 (mmp) cc_final: 0.3141 (mmp) REVERT: P 473 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7801 (tp30) REVERT: P 497 ILE cc_start: 0.8820 (mp) cc_final: 0.8286 (mt) outliers start: 1 outliers final: 0 residues processed: 1630 average time/residue: 0.6551 time to fit residues: 1879.8819 Evaluate side-chains 1292 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1292 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 727 optimal weight: 5.9990 chunk 652 optimal weight: 0.9980 chunk 362 optimal weight: 6.9990 chunk 222 optimal weight: 1.9990 chunk 440 optimal weight: 8.9990 chunk 348 optimal weight: 8.9990 chunk 674 optimal weight: 10.0000 chunk 261 optimal weight: 0.9980 chunk 410 optimal weight: 1.9990 chunk 502 optimal weight: 2.9990 chunk 781 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 80 GLN 5 113 GLN A 69 HIS ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 ASN ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 HIS ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN H 359 GLN H 383 ASN ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 187 GLN I 477 ASN ** K 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 263 GLN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN M 290 GLN M 376 GLN M 403 HIS M 481 GLN M 522 GLN N 71 HIS N 460 GLN O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 380 GLN O 452 ASN O 487 ASN P 303 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 67779 Z= 0.249 Angle : 0.757 11.739 91441 Z= 0.385 Chirality : 0.047 0.348 10955 Planarity : 0.005 0.068 11721 Dihedral : 6.857 179.501 9295 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 1.92 % Allowed : 10.56 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.09), residues: 8683 helix: 0.19 (0.07), residues: 4569 sheet: -1.77 (0.20), residues: 602 loop : -1.82 (0.10), residues: 3512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP N 495 HIS 0.020 0.001 HIS 1 45 PHE 0.041 0.002 PHE P 268 TYR 0.022 0.002 TYR P 304 ARG 0.015 0.001 ARG G 397 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1604 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1463 time to evaluate : 5.961 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: 1 117 MET cc_start: 0.5983 (mmp) cc_final: 0.5125 (mmp) REVERT: 2 49 MET cc_start: 0.5901 (mmp) cc_final: 0.5556 (tpt) REVERT: 3 63 MET cc_start: 0.2793 (mmm) cc_final: 0.2043 (mmt) REVERT: 5 105 ARG cc_start: 0.7563 (ppt170) cc_final: 0.7228 (ppt170) REVERT: 6 54 ASN cc_start: 0.4709 (t0) cc_final: 0.3817 (m110) REVERT: A 167 PHE cc_start: 0.8714 (t80) cc_final: 0.8505 (t80) REVERT: A 171 MET cc_start: 0.8309 (mtt) cc_final: 0.7160 (tpt) REVERT: A 426 TYR cc_start: 0.8700 (t80) cc_final: 0.8357 (t80) REVERT: B 114 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7482 (tm-30) REVERT: B 432 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7480 (mm-30) REVERT: B 441 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8250 (tttp) REVERT: C 40 CYS cc_start: 0.8234 (m) cc_final: 0.7927 (m) REVERT: C 110 GLU cc_start: 0.8171 (tp30) cc_final: 0.7846 (pt0) REVERT: C 152 MET cc_start: 0.6769 (mpp) cc_final: 0.6381 (mpp) REVERT: C 188 ASN cc_start: 0.6503 (t0) cc_final: 0.6099 (t0) REVERT: C 230 ARG cc_start: 0.4549 (mpp80) cc_final: 0.4060 (ttt-90) REVERT: C 305 MET cc_start: 0.5665 (ptm) cc_final: 0.4947 (mmt) REVERT: C 415 GLU cc_start: 0.9086 (mp0) cc_final: 0.8618 (mp0) REVERT: C 438 ARG cc_start: 0.7826 (ttm-80) cc_final: 0.7170 (ttm170) REVERT: C 453 GLN cc_start: 0.8683 (tm-30) cc_final: 0.8388 (tm-30) REVERT: C 473 GLU cc_start: 0.8810 (mp0) cc_final: 0.8578 (pm20) REVERT: C 476 GLU cc_start: 0.7406 (mp0) cc_final: 0.6954 (mp0) REVERT: C 497 GLU cc_start: 0.8208 (tt0) cc_final: 0.7660 (tt0) REVERT: C 499 LEU cc_start: 0.8639 (tp) cc_final: 0.8418 (tp) REVERT: D 272 MET cc_start: 0.7419 (mpp) cc_final: 0.6599 (mpp) REVERT: D 532 ILE cc_start: 0.8768 (mm) cc_final: 0.8265 (mt) REVERT: D 533 ASP cc_start: 0.6168 (m-30) cc_final: 0.5769 (m-30) REVERT: E 80 MET cc_start: 0.8203 (mmt) cc_final: 0.7991 (mmt) REVERT: E 129 HIS cc_start: 0.8171 (t70) cc_final: 0.7867 (t-170) REVERT: E 208 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6517 (pp) REVERT: E 436 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7641 (tm-30) REVERT: E 446 TYR cc_start: 0.8017 (m-80) cc_final: 0.7465 (m-80) REVERT: F 36 THR cc_start: 0.8146 (p) cc_final: 0.7529 (t) REVERT: F 145 ARG cc_start: 0.7237 (tpt170) cc_final: 0.6302 (tpt-90) REVERT: F 350 VAL cc_start: 0.8759 (t) cc_final: 0.8426 (m) REVERT: F 381 LYS cc_start: 0.8435 (mmmt) cc_final: 0.7954 (mmmm) REVERT: F 494 VAL cc_start: 0.8800 (t) cc_final: 0.8590 (t) REVERT: G 32 ILE cc_start: 0.9062 (tp) cc_final: 0.8833 (tp) REVERT: G 430 LYS cc_start: 0.8613 (ptmt) cc_final: 0.8330 (ttpt) REVERT: G 467 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6589 (ttm170) REVERT: H 85 MET cc_start: 0.8312 (mmm) cc_final: 0.8020 (tpt) REVERT: H 94 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8099 (tm-30) REVERT: H 138 LYS cc_start: 0.6846 (ttmt) cc_final: 0.6504 (ttpt) REVERT: H 347 CYS cc_start: 0.6112 (m) cc_final: 0.5194 (p) REVERT: H 387 ASP cc_start: 0.8183 (t0) cc_final: 0.7938 (t0) REVERT: H 404 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.8022 (ttp-110) REVERT: H 523 GLN cc_start: 0.8263 (tt0) cc_final: 0.7468 (tt0) REVERT: I 36 LEU cc_start: 0.8692 (tp) cc_final: 0.8458 (tp) REVERT: I 99 GLU cc_start: 0.7064 (tp30) cc_final: 0.6159 (tp30) REVERT: I 148 LEU cc_start: 0.6958 (mp) cc_final: 0.6526 (tt) REVERT: I 206 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6926 (tmm) REVERT: I 400 LYS cc_start: 0.7559 (tmtt) cc_final: 0.7318 (tttt) REVERT: J 87 MET cc_start: 0.6662 (tpt) cc_final: 0.6420 (tpt) REVERT: J 244 MET cc_start: -0.0696 (mtt) cc_final: -0.4111 (mpp) REVERT: K 400 ASN cc_start: 0.6710 (OUTLIER) cc_final: 0.6481 (p0) REVERT: L 115 SER cc_start: 0.8405 (m) cc_final: 0.8026 (t) REVERT: L 151 MET cc_start: 0.4907 (OUTLIER) cc_final: 0.4607 (tpp) REVERT: L 496 ARG cc_start: 0.5533 (mmt180) cc_final: 0.5304 (mmt180) REVERT: M 39 MET cc_start: 0.7915 (mmm) cc_final: 0.7708 (mmm) REVERT: M 485 MET cc_start: 0.7631 (mmm) cc_final: 0.7283 (mmp) REVERT: N 71 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5320 (m-70) REVERT: N 190 MET cc_start: 0.5892 (mpp) cc_final: 0.5670 (mpp) REVERT: N 221 MET cc_start: 0.3369 (OUTLIER) cc_final: 0.2914 (mtt) REVERT: N 461 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7210 (tp30) REVERT: N 503 GLN cc_start: 0.8755 (tp40) cc_final: 0.7755 (tm-30) REVERT: O 65 ILE cc_start: 0.8957 (pt) cc_final: 0.8651 (pt) REVERT: O 494 GLU cc_start: 0.7331 (mm-30) cc_final: 0.6944 (mm-30) REVERT: P 84 LYS cc_start: 0.7872 (tmtt) cc_final: 0.7078 (ttmt) REVERT: P 266 MET cc_start: 0.6562 (mmp) cc_final: 0.5894 (mmp) REVERT: P 344 MET cc_start: 0.3608 (mmp) cc_final: 0.2844 (mmp) REVERT: P 400 LYS cc_start: 0.7717 (tptt) cc_final: 0.7437 (tptp) REVERT: P 473 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7744 (tp30) REVERT: P 497 ILE cc_start: 0.8730 (mp) cc_final: 0.8133 (mm) REVERT: P 526 MET cc_start: 0.5975 (mtt) cc_final: 0.5744 (mtt) outliers start: 141 outliers final: 82 residues processed: 1526 average time/residue: 0.6054 time to fit residues: 1608.8833 Evaluate side-chains 1389 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1298 time to evaluate : 5.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 77 HIS Chi-restraints excluded: chain 1 residue 94 LEU Chi-restraints excluded: chain 5 residue 28 PHE Chi-restraints excluded: chain 5 residue 103 PHE Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 123 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 255 PHE Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 453 GLN Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 508 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 193 LYS Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 345 CYS Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 206 MET Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 518 THR Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain K residue 400 ASN Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 151 MET Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 91 MET Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 524 VAL Chi-restraints excluded: chain N residue 71 HIS Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 459 LEU Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 360 PHE Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 470 VAL Chi-restraints excluded: chain P residue 498 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 434 optimal weight: 20.0000 chunk 242 optimal weight: 8.9990 chunk 650 optimal weight: 0.8980 chunk 532 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 783 optimal weight: 20.0000 chunk 846 optimal weight: 5.9990 chunk 697 optimal weight: 6.9990 chunk 776 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 628 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS D 350 GLN E 122 GLN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN H 201 ASN ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 475 GLN I 477 ASN K 74 HIS ** K 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 396 GLN K 474 ASN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 502 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN M 139 GLN M 411 ASN M 481 GLN M 516 GLN N 320 ASN O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 HIS ** O 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 67779 Z= 0.338 Angle : 0.769 13.228 91441 Z= 0.392 Chirality : 0.047 0.262 10955 Planarity : 0.005 0.067 11721 Dihedral : 6.644 159.321 9295 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.94 % Rotamer: Outliers : 3.01 % Allowed : 14.62 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.26 (0.09), residues: 8683 helix: 0.11 (0.07), residues: 4564 sheet: -1.86 (0.20), residues: 619 loop : -1.87 (0.10), residues: 3500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 496 HIS 0.031 0.002 HIS N 71 PHE 0.036 0.002 PHE O 175 TYR 0.030 0.002 TYR O 438 ARG 0.012 0.001 ARG G 397 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1647 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1426 time to evaluate : 6.044 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: 1 67 MET cc_start: 0.7748 (pmm) cc_final: 0.7513 (pmm) REVERT: 1 117 MET cc_start: 0.5915 (mmp) cc_final: 0.5182 (mmp) REVERT: 6 30 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7740 (tpm170) REVERT: 6 54 ASN cc_start: 0.4730 (t0) cc_final: 0.3698 (m110) REVERT: A 167 PHE cc_start: 0.8818 (t80) cc_final: 0.8606 (t80) REVERT: A 171 MET cc_start: 0.8315 (mtt) cc_final: 0.7287 (tpt) REVERT: B 87 MET cc_start: 0.8197 (mmm) cc_final: 0.7744 (mmm) REVERT: B 114 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 441 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.8238 (tttp) REVERT: C 40 CYS cc_start: 0.8170 (m) cc_final: 0.7882 (m) REVERT: C 48 LYS cc_start: 0.8341 (mmmm) cc_final: 0.8110 (mmmt) REVERT: C 110 GLU cc_start: 0.8252 (tp30) cc_final: 0.7868 (pt0) REVERT: C 145 ASP cc_start: 0.6135 (OUTLIER) cc_final: 0.5683 (t0) REVERT: C 152 MET cc_start: 0.6940 (mpp) cc_final: 0.6702 (mpp) REVERT: C 188 ASN cc_start: 0.6730 (t0) cc_final: 0.6267 (t0) REVERT: C 230 ARG cc_start: 0.4592 (mpp80) cc_final: 0.4122 (ttt-90) REVERT: C 305 MET cc_start: 0.5895 (ptm) cc_final: 0.5111 (mmt) REVERT: C 416 MET cc_start: 0.8264 (mmm) cc_final: 0.7950 (mmm) REVERT: C 453 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8192 (tm-30) REVERT: C 473 GLU cc_start: 0.8843 (mp0) cc_final: 0.8557 (pm20) REVERT: C 476 GLU cc_start: 0.7546 (mp0) cc_final: 0.7040 (mp0) REVERT: D 533 ASP cc_start: 0.6830 (m-30) cc_final: 0.6299 (m-30) REVERT: E 55 ASN cc_start: 0.7682 (t0) cc_final: 0.7427 (t0) REVERT: E 208 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6786 (pp) REVERT: E 436 GLU cc_start: 0.7926 (tm-30) cc_final: 0.7653 (tm-30) REVERT: F 28 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7804 (mmm-85) REVERT: F 36 THR cc_start: 0.8194 (p) cc_final: 0.7524 (t) REVERT: F 44 MET cc_start: 0.5867 (mmm) cc_final: 0.5631 (mmt) REVERT: F 145 ARG cc_start: 0.7221 (tpt170) cc_final: 0.6231 (tpt-90) REVERT: F 150 ASP cc_start: 0.8619 (m-30) cc_final: 0.8104 (t0) REVERT: F 381 LYS cc_start: 0.8508 (mmmt) cc_final: 0.8016 (mmmm) REVERT: F 418 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7960 (ptm) REVERT: F 494 VAL cc_start: 0.8750 (t) cc_final: 0.8533 (t) REVERT: G 32 ILE cc_start: 0.9105 (tp) cc_final: 0.8862 (tp) REVERT: G 55 LYS cc_start: 0.8033 (tppt) cc_final: 0.7819 (tppt) REVERT: G 467 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6992 (ttm170) REVERT: G 477 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.7977 (p) REVERT: H 347 CYS cc_start: 0.6343 (m) cc_final: 0.5186 (p) REVERT: H 387 ASP cc_start: 0.8199 (t0) cc_final: 0.7992 (t0) REVERT: H 404 ARG cc_start: 0.8295 (mtm-85) cc_final: 0.8048 (ttp-110) REVERT: I 36 LEU cc_start: 0.8584 (tp) cc_final: 0.8312 (tp) REVERT: I 148 LEU cc_start: 0.7185 (mp) cc_final: 0.6652 (tt) REVERT: I 206 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6853 (tmm) REVERT: I 225 MET cc_start: 0.1894 (ppp) cc_final: 0.1355 (ptt) REVERT: J 87 MET cc_start: 0.7668 (tpt) cc_final: 0.6669 (tpt) REVERT: J 135 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8858 (tptp) REVERT: J 244 MET cc_start: -0.0564 (mtt) cc_final: -0.3864 (mpp) REVERT: K 400 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6818 (p0) REVERT: L 115 SER cc_start: 0.8559 (m) cc_final: 0.8065 (t) REVERT: L 120 CYS cc_start: 0.8240 (t) cc_final: 0.7684 (t) REVERT: L 210 ILE cc_start: 0.8175 (mt) cc_final: 0.7971 (mt) REVERT: L 320 MET cc_start: 0.4349 (ptm) cc_final: 0.3827 (ppp) REVERT: L 355 MET cc_start: 0.4373 (ppp) cc_final: 0.4085 (ppp) REVERT: M 39 MET cc_start: 0.7942 (mmm) cc_final: 0.7633 (mmm) REVERT: M 119 GLU cc_start: 0.7851 (tp30) cc_final: 0.7553 (tp30) REVERT: M 476 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7701 (mt-10) REVERT: M 516 GLN cc_start: 0.8327 (tt0) cc_final: 0.8020 (tt0) REVERT: N 124 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7985 (tm-30) REVERT: N 187 ASP cc_start: 0.6816 (t0) cc_final: 0.6565 (m-30) REVERT: N 221 MET cc_start: 0.3373 (OUTLIER) cc_final: 0.2868 (mtt) REVERT: N 449 LYS cc_start: 0.8972 (mttt) cc_final: 0.8645 (mttm) REVERT: N 461 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7233 (tp30) REVERT: N 503 GLN cc_start: 0.8819 (tp40) cc_final: 0.7780 (tm-30) REVERT: O 65 ILE cc_start: 0.8972 (pt) cc_final: 0.8717 (pt) REVERT: O 194 MET cc_start: 0.6558 (mmm) cc_final: 0.6245 (tpp) REVERT: O 301 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8328 (mm110) REVERT: O 494 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7154 (mm-30) REVERT: O 499 ARG cc_start: 0.6666 (ttt90) cc_final: 0.6367 (ttt90) REVERT: P 84 LYS cc_start: 0.8009 (tmtt) cc_final: 0.7190 (tmtt) REVERT: P 266 MET cc_start: 0.6566 (mmp) cc_final: 0.5825 (mmp) REVERT: P 272 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: P 344 MET cc_start: 0.3583 (mmp) cc_final: 0.2828 (mmp) REVERT: P 473 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7673 (tp30) REVERT: P 504 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8150 (tppt) outliers start: 221 outliers final: 142 residues processed: 1548 average time/residue: 0.6022 time to fit residues: 1629.3357 Evaluate side-chains 1451 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1297 time to evaluate : 5.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 14 THR Chi-restraints excluded: chain 1 residue 56 ASP Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 1 residue 94 LEU Chi-restraints excluded: chain 1 residue 100 TYR Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 53 LEU Chi-restraints excluded: chain 6 residue 30 ARG Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 418 MET Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 345 CYS Chi-restraints excluded: chain G residue 381 PHE Chi-restraints excluded: chain G residue 382 MET Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 383 ASN Chi-restraints excluded: chain H residue 471 HIS Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 19 SER Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 206 MET Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 458 GLN Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 518 THR Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 428 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 400 ASN Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 459 THR Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 297 VAL Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 71 HIS Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 221 MET Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 471 SER Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain N residue 509 THR Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 301 GLN Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 360 PHE Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 470 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 773 optimal weight: 1.9990 chunk 588 optimal weight: 0.1980 chunk 406 optimal weight: 0.6980 chunk 86 optimal weight: 30.0000 chunk 373 optimal weight: 4.9990 chunk 525 optimal weight: 0.9990 chunk 786 optimal weight: 10.0000 chunk 832 optimal weight: 20.0000 chunk 410 optimal weight: 0.4980 chunk 745 optimal weight: 0.5980 chunk 224 optimal weight: 5.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS D 468 ASN E 122 GLN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** I 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN K 74 HIS K 277 GLN ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN L 301 GLN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN M 376 GLN O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS P 435 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 67779 Z= 0.195 Angle : 0.716 13.268 91441 Z= 0.357 Chirality : 0.045 0.372 10955 Planarity : 0.004 0.118 11721 Dihedral : 6.264 150.118 9295 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 3.19 % Allowed : 17.37 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.11 (0.09), residues: 8683 helix: 0.26 (0.07), residues: 4579 sheet: -1.89 (0.20), residues: 650 loop : -1.83 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 496 HIS 0.010 0.001 HIS 1 45 PHE 0.043 0.002 PHE J 179 TYR 0.019 0.002 TYR D 179 ARG 0.016 0.001 ARG 6 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1694 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1460 time to evaluate : 6.045 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: 1 89 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6779 (tm-30) REVERT: 1 117 MET cc_start: 0.5955 (mmp) cc_final: 0.5301 (mmp) REVERT: 2 49 MET cc_start: 0.5805 (mmp) cc_final: 0.5444 (tpt) REVERT: 3 63 MET cc_start: 0.2521 (mmm) cc_final: 0.1730 (mmt) REVERT: 3 106 LEU cc_start: 0.8027 (mt) cc_final: 0.6699 (pp) REVERT: 5 103 PHE cc_start: 0.4840 (t80) cc_final: 0.4559 (t80) REVERT: 5 115 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7565 (tm-30) REVERT: 5 117 ILE cc_start: 0.6219 (mm) cc_final: 0.5809 (mm) REVERT: 6 54 ASN cc_start: 0.4584 (t0) cc_final: 0.3782 (m110) REVERT: A 171 MET cc_start: 0.8268 (mtt) cc_final: 0.7274 (tpt) REVERT: A 426 TYR cc_start: 0.8617 (t80) cc_final: 0.8291 (t80) REVERT: B 114 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 138 ARG cc_start: 0.8036 (tmm-80) cc_final: 0.7803 (tmm-80) REVERT: B 504 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8552 (tp) REVERT: C 40 CYS cc_start: 0.8114 (m) cc_final: 0.7767 (m) REVERT: C 110 GLU cc_start: 0.8155 (tp30) cc_final: 0.7780 (pt0) REVERT: C 152 MET cc_start: 0.6806 (mpp) cc_final: 0.6501 (mpp) REVERT: C 188 ASN cc_start: 0.6525 (t0) cc_final: 0.6085 (t0) REVERT: C 416 MET cc_start: 0.8286 (mmm) cc_final: 0.7920 (mmm) REVERT: C 453 GLN cc_start: 0.8569 (tm-30) cc_final: 0.7840 (tm-30) REVERT: C 461 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7418 (ttm-80) REVERT: C 473 GLU cc_start: 0.8812 (mp0) cc_final: 0.8527 (pm20) REVERT: C 476 GLU cc_start: 0.7568 (mp0) cc_final: 0.7103 (mp0) REVERT: D 533 ASP cc_start: 0.6532 (m-30) cc_final: 0.6008 (m-30) REVERT: E 208 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6622 (pp) REVERT: E 436 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7552 (tm-30) REVERT: E 446 TYR cc_start: 0.8166 (m-80) cc_final: 0.7951 (m-80) REVERT: E 515 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8523 (mm-40) REVERT: F 28 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7842 (mmm-85) REVERT: F 36 THR cc_start: 0.8072 (p) cc_final: 0.7461 (t) REVERT: F 143 MET cc_start: 0.5201 (mmp) cc_final: 0.4928 (mtt) REVERT: F 145 ARG cc_start: 0.7253 (tpt170) cc_final: 0.6257 (tpt-90) REVERT: F 150 ASP cc_start: 0.8628 (m-30) cc_final: 0.8208 (t0) REVERT: F 342 ASP cc_start: 0.6841 (p0) cc_final: 0.6589 (p0) REVERT: F 381 LYS cc_start: 0.8445 (mmmt) cc_final: 0.7969 (mmmm) REVERT: F 494 VAL cc_start: 0.8686 (t) cc_final: 0.8446 (t) REVERT: G 430 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8289 (ttpt) REVERT: G 467 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6446 (ttm170) REVERT: G 477 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7789 (p) REVERT: G 514 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8760 (p) REVERT: H 347 CYS cc_start: 0.6046 (m) cc_final: 0.5620 (p) REVERT: I 36 LEU cc_start: 0.8575 (tp) cc_final: 0.8300 (tp) REVERT: I 99 GLU cc_start: 0.7200 (tp30) cc_final: 0.6593 (tp30) REVERT: I 102 LYS cc_start: 0.7844 (ttpt) cc_final: 0.7475 (ttpt) REVERT: I 148 LEU cc_start: 0.7147 (mp) cc_final: 0.6636 (tt) REVERT: I 206 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6829 (tmm) REVERT: I 225 MET cc_start: 0.1722 (OUTLIER) cc_final: 0.1301 (ptt) REVERT: I 400 LYS cc_start: 0.7349 (tmtt) cc_final: 0.7112 (tttt) REVERT: J 72 LYS cc_start: 0.8863 (mmmt) cc_final: 0.8604 (mmmm) REVERT: J 244 MET cc_start: -0.0828 (mtt) cc_final: -0.4353 (mpp) REVERT: J 441 LYS cc_start: 0.8619 (tttp) cc_final: 0.8236 (ttmm) REVERT: J 502 GLN cc_start: 0.7956 (tp40) cc_final: 0.7727 (tp40) REVERT: K 20 ARG cc_start: 0.6917 (tpp-160) cc_final: 0.6140 (tpt170) REVERT: K 64 ASN cc_start: 0.7010 (p0) cc_final: 0.6777 (p0) REVERT: K 400 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6521 (p0) REVERT: K 422 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8137 (tp) REVERT: L 115 SER cc_start: 0.8447 (m) cc_final: 0.8054 (t) REVERT: L 120 CYS cc_start: 0.7971 (t) cc_final: 0.7493 (t) REVERT: L 320 MET cc_start: 0.4153 (ptm) cc_final: 0.3772 (ppp) REVERT: L 355 MET cc_start: 0.4698 (ppp) cc_final: 0.4472 (tmm) REVERT: L 489 LYS cc_start: 0.6558 (mttt) cc_final: 0.6353 (mtmt) REVERT: L 496 ARG cc_start: 0.5389 (mmt180) cc_final: 0.5171 (mmt180) REVERT: M 39 MET cc_start: 0.7887 (mmm) cc_final: 0.7540 (mmm) REVERT: M 89 LYS cc_start: 0.8667 (tppt) cc_final: 0.8446 (ttpt) REVERT: M 93 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7805 (tm-30) REVERT: M 119 GLU cc_start: 0.7813 (tp30) cc_final: 0.7488 (tp30) REVERT: M 158 ASP cc_start: 0.6855 (t0) cc_final: 0.6058 (t0) REVERT: M 341 ILE cc_start: 0.7753 (tp) cc_final: 0.7478 (tp) REVERT: M 476 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7692 (mt-10) REVERT: M 485 MET cc_start: 0.7619 (mmm) cc_final: 0.7279 (mmp) REVERT: M 505 HIS cc_start: 0.5928 (t70) cc_final: 0.5427 (t70) REVERT: N 71 HIS cc_start: 0.5998 (OUTLIER) cc_final: 0.4977 (m90) REVERT: N 124 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7970 (tm-30) REVERT: N 190 MET cc_start: 0.6628 (mpp) cc_final: 0.6313 (mpp) REVERT: N 376 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7117 (pp) REVERT: N 503 GLN cc_start: 0.8775 (tp40) cc_final: 0.7775 (tm-30) REVERT: O 65 ILE cc_start: 0.8889 (pt) cc_final: 0.8589 (pt) REVERT: O 494 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6842 (mm-30) REVERT: O 499 ARG cc_start: 0.6421 (ttt90) cc_final: 0.6109 (ttt90) REVERT: P 75 GLU cc_start: 0.8045 (tp30) cc_final: 0.7775 (tp30) REVERT: P 84 LYS cc_start: 0.7872 (tmtt) cc_final: 0.7026 (ttmt) REVERT: P 224 LYS cc_start: 0.6578 (pttm) cc_final: 0.6070 (ptmm) REVERT: P 266 MET cc_start: 0.6453 (mmp) cc_final: 0.5707 (mmp) REVERT: P 272 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: P 344 MET cc_start: 0.3936 (mmp) cc_final: 0.3251 (mmp) REVERT: P 473 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7381 (tp30) REVERT: P 497 ILE cc_start: 0.8620 (mp) cc_final: 0.8064 (mt) outliers start: 234 outliers final: 127 residues processed: 1591 average time/residue: 0.6004 time to fit residues: 1652.6540 Evaluate side-chains 1450 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 1310 time to evaluate : 5.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 1 residue 89 GLU Chi-restraints excluded: chain 3 residue 86 GLU Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 53 LEU Chi-restraints excluded: chain 5 residue 102 PHE Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 453 GLN Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 345 CYS Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 382 MET Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 206 MET Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 415 MET Chi-restraints excluded: chain J residue 509 GLU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain K residue 400 ASN Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 422 LEU Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 443 LEU Chi-restraints excluded: chain L residue 465 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 521 THR Chi-restraints excluded: chain N residue 71 HIS Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 437 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 301 GLN Chi-restraints excluded: chain O residue 332 THR Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 468 TYR Chi-restraints excluded: chain P residue 499 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 693 optimal weight: 20.0000 chunk 472 optimal weight: 0.0070 chunk 12 optimal weight: 30.0000 chunk 619 optimal weight: 0.6980 chunk 343 optimal weight: 10.0000 chunk 710 optimal weight: 0.8980 chunk 575 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 424 optimal weight: 10.0000 chunk 747 optimal weight: 7.9990 chunk 210 optimal weight: 0.6980 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 HIS ** 2 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 113 GLN A 69 HIS ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 HIS D 285 ASN E 55 ASN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN I 477 ASN K 74 HIS ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN L 301 GLN ** L 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 411 ASN O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 67779 Z= 0.214 Angle : 0.712 13.111 91441 Z= 0.355 Chirality : 0.045 0.275 10955 Planarity : 0.004 0.060 11721 Dihedral : 6.079 145.114 9295 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.41 % Favored : 94.56 % Rotamer: Outliers : 3.10 % Allowed : 19.23 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.09), residues: 8683 helix: 0.34 (0.07), residues: 4565 sheet: -1.82 (0.20), residues: 643 loop : -1.83 (0.10), residues: 3475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 126 HIS 0.017 0.001 HIS J 175 PHE 0.028 0.002 PHE G 216 TYR 0.025 0.002 TYR L 449 ARG 0.009 0.000 ARG C 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1382 time to evaluate : 5.953 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: 1 89 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6732 (tm-30) REVERT: 1 117 MET cc_start: 0.5909 (mmp) cc_final: 0.5217 (mmp) REVERT: 3 106 LEU cc_start: 0.8280 (mt) cc_final: 0.7079 (pp) REVERT: 4 95 GLN cc_start: 0.7256 (pp30) cc_final: 0.6914 (tp40) REVERT: 6 54 ASN cc_start: 0.4363 (t0) cc_final: 0.3725 (m110) REVERT: A 167 PHE cc_start: 0.8786 (t80) cc_final: 0.8513 (t80) REVERT: A 171 MET cc_start: 0.8193 (mtt) cc_final: 0.7275 (tpt) REVERT: A 426 TYR cc_start: 0.8713 (t80) cc_final: 0.8404 (t80) REVERT: B 48 MET cc_start: 0.8745 (ttp) cc_final: 0.8367 (ttp) REVERT: B 114 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 138 ARG cc_start: 0.8078 (tmm-80) cc_final: 0.7864 (tmm-80) REVERT: B 504 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8592 (tp) REVERT: C 38 ARG cc_start: 0.8371 (ttm110) cc_final: 0.8038 (ttm110) REVERT: C 40 CYS cc_start: 0.8087 (m) cc_final: 0.7777 (m) REVERT: C 54 MET cc_start: 0.7173 (ptm) cc_final: 0.6949 (ppp) REVERT: C 110 GLU cc_start: 0.8177 (tp30) cc_final: 0.7785 (pt0) REVERT: C 152 MET cc_start: 0.6892 (mpp) cc_final: 0.6582 (mpp) REVERT: C 188 ASN cc_start: 0.6566 (t0) cc_final: 0.6089 (t0) REVERT: C 229 MET cc_start: 0.4184 (ptp) cc_final: 0.3971 (ptp) REVERT: C 453 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7828 (tm-30) REVERT: C 461 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7497 (ttm-80) REVERT: C 473 GLU cc_start: 0.8809 (mp0) cc_final: 0.8509 (pm20) REVERT: C 476 GLU cc_start: 0.7570 (mp0) cc_final: 0.7097 (mp0) REVERT: C 497 GLU cc_start: 0.8230 (tt0) cc_final: 0.7483 (tt0) REVERT: C 504 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7407 (tm-30) REVERT: D 532 ILE cc_start: 0.8759 (mm) cc_final: 0.8258 (mt) REVERT: D 533 ASP cc_start: 0.6628 (m-30) cc_final: 0.6354 (m-30) REVERT: E 207 GLU cc_start: 0.6963 (pp20) cc_final: 0.6661 (pp20) REVERT: E 208 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6369 (pp) REVERT: E 436 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7664 (tm-30) REVERT: E 444 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7160 (mt-10) REVERT: E 515 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8530 (mm-40) REVERT: F 36 THR cc_start: 0.8070 (p) cc_final: 0.7580 (t) REVERT: F 143 MET cc_start: 0.5335 (mmp) cc_final: 0.5113 (mtt) REVERT: F 145 ARG cc_start: 0.7166 (tpt170) cc_final: 0.6220 (tpt-90) REVERT: F 150 ASP cc_start: 0.8652 (m-30) cc_final: 0.8213 (t0) REVERT: F 195 GLU cc_start: 0.7992 (mp0) cc_final: 0.6808 (mt-10) REVERT: F 381 LYS cc_start: 0.8455 (mmmt) cc_final: 0.7976 (mmmm) REVERT: F 494 VAL cc_start: 0.8695 (t) cc_final: 0.8473 (t) REVERT: G 73 HIS cc_start: 0.7668 (t-90) cc_final: 0.7396 (t-90) REVERT: G 185 MET cc_start: 0.4631 (OUTLIER) cc_final: 0.3255 (ppp) REVERT: G 430 LYS cc_start: 0.8501 (ptmt) cc_final: 0.8224 (ttpt) REVERT: G 467 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6392 (ttm170) REVERT: G 477 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7840 (p) REVERT: G 514 VAL cc_start: 0.9018 (OUTLIER) cc_final: 0.8713 (p) REVERT: G 518 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7226 (mm-30) REVERT: H 85 MET cc_start: 0.8220 (mmm) cc_final: 0.7726 (tpt) REVERT: H 88 MET cc_start: 0.7550 (mtm) cc_final: 0.6798 (mpp) REVERT: H 127 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6947 (mm-30) REVERT: H 347 CYS cc_start: 0.6120 (m) cc_final: 0.5553 (p) REVERT: H 468 TYR cc_start: 0.7213 (t80) cc_final: 0.6889 (m-80) REVERT: I 36 LEU cc_start: 0.8520 (tp) cc_final: 0.8195 (tp) REVERT: I 57 ASP cc_start: 0.7071 (t0) cc_final: 0.6866 (t0) REVERT: I 102 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7543 (ttpt) REVERT: I 127 GLU cc_start: 0.8256 (tp30) cc_final: 0.7752 (tp30) REVERT: I 148 LEU cc_start: 0.7092 (mp) cc_final: 0.6671 (tt) REVERT: I 206 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6870 (tmm) REVERT: I 225 MET cc_start: 0.1613 (OUTLIER) cc_final: 0.1409 (ptt) REVERT: J 72 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8563 (mmmm) REVERT: K 20 ARG cc_start: 0.6855 (tpp-160) cc_final: 0.6116 (tpt170) REVERT: K 305 MET cc_start: 0.6600 (mmp) cc_final: 0.3538 (pmm) REVERT: K 400 ASN cc_start: 0.6833 (OUTLIER) cc_final: 0.6459 (p0) REVERT: K 492 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: L 115 SER cc_start: 0.8477 (m) cc_final: 0.8047 (t) REVERT: L 120 CYS cc_start: 0.7960 (t) cc_final: 0.7465 (t) REVERT: L 320 MET cc_start: 0.4114 (OUTLIER) cc_final: 0.3635 (ppp) REVERT: M 39 MET cc_start: 0.7958 (mmm) cc_final: 0.7604 (mmm) REVERT: M 119 GLU cc_start: 0.7823 (tp30) cc_final: 0.7525 (tp30) REVERT: M 158 ASP cc_start: 0.6946 (t0) cc_final: 0.6138 (t0) REVERT: M 341 ILE cc_start: 0.7862 (tp) cc_final: 0.7572 (tp) REVERT: M 476 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7825 (mt-10) REVERT: M 485 MET cc_start: 0.7668 (mmm) cc_final: 0.7328 (mmp) REVERT: M 505 HIS cc_start: 0.5975 (t70) cc_final: 0.5322 (t70) REVERT: N 71 HIS cc_start: 0.5926 (OUTLIER) cc_final: 0.5022 (m90) REVERT: N 79 LYS cc_start: 0.8449 (pttt) cc_final: 0.8137 (ptpt) REVERT: N 124 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7963 (tm-30) REVERT: N 376 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7212 (pp) REVERT: N 503 GLN cc_start: 0.8790 (tp40) cc_final: 0.7807 (tm-30) REVERT: O 65 ILE cc_start: 0.8906 (pt) cc_final: 0.8601 (pt) REVERT: O 382 MET cc_start: 0.3126 (OUTLIER) cc_final: 0.2782 (mpp) REVERT: P 75 GLU cc_start: 0.8039 (tp30) cc_final: 0.7715 (tp30) REVERT: P 84 LYS cc_start: 0.7894 (tmtt) cc_final: 0.7058 (ttmt) REVERT: P 224 LYS cc_start: 0.6606 (pttm) cc_final: 0.6241 (ptmm) REVERT: P 266 MET cc_start: 0.6358 (mmp) cc_final: 0.5672 (mmp) REVERT: P 272 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6710 (mt-10) REVERT: P 344 MET cc_start: 0.4125 (mmp) cc_final: 0.3430 (mmp) REVERT: P 389 GLU cc_start: 0.8823 (tp30) cc_final: 0.8162 (tp30) REVERT: P 473 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7393 (tp30) REVERT: P 497 ILE cc_start: 0.8605 (mp) cc_final: 0.8130 (mt) outliers start: 227 outliers final: 143 residues processed: 1513 average time/residue: 0.5883 time to fit residues: 1557.5091 Evaluate side-chains 1464 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 1305 time to evaluate : 5.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 1 residue 89 GLU Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 77 HIS Chi-restraints excluded: chain 5 residue 102 PHE Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 453 GLN Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 345 CYS Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 471 HIS Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 206 MET Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 508 ILE Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 399 GLN Chi-restraints excluded: chain J residue 509 GLU Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 400 ASN Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 459 THR Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 297 VAL Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 465 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 508 VAL Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain N residue 71 HIS Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 437 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain N residue 508 CYS Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 301 GLN Chi-restraints excluded: chain O residue 332 THR Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 382 MET Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 468 TYR Chi-restraints excluded: chain P residue 499 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 280 optimal weight: 7.9990 chunk 749 optimal weight: 6.9990 chunk 164 optimal weight: 0.0270 chunk 488 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 833 optimal weight: 0.0170 chunk 691 optimal weight: 8.9990 chunk 385 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 275 optimal weight: 5.9990 chunk 437 optimal weight: 6.9990 overall best weight: 2.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 500 GLN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** I 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 434 GLN L 250 GLN L 301 GLN L 350 GLN M 122 GLN N 71 HIS O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS P 359 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 67779 Z= 0.256 Angle : 0.721 12.983 91441 Z= 0.360 Chirality : 0.045 0.326 10955 Planarity : 0.004 0.066 11721 Dihedral : 6.020 140.189 9295 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 3.53 % Allowed : 20.29 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.09), residues: 8683 helix: 0.35 (0.07), residues: 4568 sheet: -1.83 (0.20), residues: 664 loop : -1.82 (0.10), residues: 3451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 435 HIS 0.031 0.001 HIS C 470 PHE 0.062 0.002 PHE J 179 TYR 0.028 0.002 TYR K 437 ARG 0.016 0.001 ARG M 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1372 time to evaluate : 6.105 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: 1 89 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: 3 63 MET cc_start: 0.2613 (mmm) cc_final: 0.1809 (mmt) REVERT: 3 106 LEU cc_start: 0.8380 (mt) cc_final: 0.7045 (pp) REVERT: 6 54 ASN cc_start: 0.4239 (m-40) cc_final: 0.3694 (m110) REVERT: A 167 PHE cc_start: 0.8802 (t80) cc_final: 0.8555 (t80) REVERT: A 171 MET cc_start: 0.8259 (mtt) cc_final: 0.7351 (tpt) REVERT: B 48 MET cc_start: 0.8732 (ttp) cc_final: 0.8351 (ttp) REVERT: B 52 LEU cc_start: 0.8893 (mm) cc_final: 0.8679 (mm) REVERT: B 109 LEU cc_start: 0.8986 (mp) cc_final: 0.8751 (mp) REVERT: B 138 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7880 (tmm-80) REVERT: B 504 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8591 (tp) REVERT: C 38 ARG cc_start: 0.8432 (ttm110) cc_final: 0.8105 (ttm110) REVERT: C 40 CYS cc_start: 0.8014 (m) cc_final: 0.7708 (m) REVERT: C 152 MET cc_start: 0.6987 (mpp) cc_final: 0.6673 (mpp) REVERT: C 188 ASN cc_start: 0.6444 (t0) cc_final: 0.5938 (t0) REVERT: C 453 GLN cc_start: 0.8731 (tm-30) cc_final: 0.7981 (tm-30) REVERT: C 476 GLU cc_start: 0.7570 (mp0) cc_final: 0.7126 (mp0) REVERT: C 504 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7437 (tm-30) REVERT: D 429 GLU cc_start: 0.7866 (mp0) cc_final: 0.7638 (mp0) REVERT: D 533 ASP cc_start: 0.6939 (m-30) cc_final: 0.6605 (m-30) REVERT: E 91 MET cc_start: 0.8979 (tpp) cc_final: 0.8727 (mmm) REVERT: E 208 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6587 (pp) REVERT: E 436 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7685 (tm-30) REVERT: F 36 THR cc_start: 0.8167 (p) cc_final: 0.7629 (t) REVERT: F 43 THR cc_start: 0.7643 (p) cc_final: 0.7062 (p) REVERT: F 145 ARG cc_start: 0.7213 (tpt170) cc_final: 0.6337 (tpt-90) REVERT: F 150 ASP cc_start: 0.8669 (m-30) cc_final: 0.8222 (t0) REVERT: F 190 MET cc_start: 0.6509 (pmm) cc_final: 0.6102 (pmm) REVERT: F 195 GLU cc_start: 0.8008 (mp0) cc_final: 0.6941 (mt-10) REVERT: F 342 ASP cc_start: 0.6679 (p0) cc_final: 0.6438 (p0) REVERT: F 381 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8018 (mmmm) REVERT: F 494 VAL cc_start: 0.8714 (t) cc_final: 0.8504 (t) REVERT: F 522 MET cc_start: 0.8005 (mmm) cc_final: 0.7708 (mmp) REVERT: G 185 MET cc_start: 0.4688 (OUTLIER) cc_final: 0.3532 (ppp) REVERT: G 430 LYS cc_start: 0.8471 (ptmt) cc_final: 0.8188 (ttpt) REVERT: G 467 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.6445 (ttm170) REVERT: G 468 HIS cc_start: 0.7881 (OUTLIER) cc_final: 0.7359 (t-170) REVERT: G 477 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.7979 (p) REVERT: G 514 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8763 (p) REVERT: H 166 THR cc_start: 0.8802 (t) cc_final: 0.8531 (m) REVERT: H 347 CYS cc_start: 0.6143 (m) cc_final: 0.5675 (p) REVERT: H 468 TYR cc_start: 0.7321 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: I 36 LEU cc_start: 0.8536 (tp) cc_final: 0.8230 (tp) REVERT: I 99 GLU cc_start: 0.7152 (tp30) cc_final: 0.6946 (tp30) REVERT: I 127 GLU cc_start: 0.8289 (tp30) cc_final: 0.7825 (tp30) REVERT: I 148 LEU cc_start: 0.7122 (mp) cc_final: 0.6719 (tt) REVERT: I 225 MET cc_start: 0.1385 (OUTLIER) cc_final: 0.1006 (ptt) REVERT: I 246 MET cc_start: 0.3064 (mmt) cc_final: 0.0597 (mtm) REVERT: J 72 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8553 (mmmm) REVERT: J 112 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7363 (mm-30) REVERT: J 441 LYS cc_start: 0.8650 (tttp) cc_final: 0.8193 (tttp) REVERT: K 305 MET cc_start: 0.6619 (mmp) cc_final: 0.3612 (pmm) REVERT: K 400 ASN cc_start: 0.6912 (OUTLIER) cc_final: 0.6451 (p0) REVERT: K 492 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7205 (pm20) REVERT: L 115 SER cc_start: 0.8536 (m) cc_final: 0.8069 (t) REVERT: L 120 CYS cc_start: 0.8041 (t) cc_final: 0.7560 (t) REVERT: L 126 LYS cc_start: 0.7614 (ttmm) cc_final: 0.7345 (ttpt) REVERT: M 39 MET cc_start: 0.7934 (mmm) cc_final: 0.7582 (mmm) REVERT: M 89 LYS cc_start: 0.8731 (tppt) cc_final: 0.8464 (ttpt) REVERT: M 119 GLU cc_start: 0.7766 (tp30) cc_final: 0.7536 (tp30) REVERT: M 132 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7479 (mmm-85) REVERT: M 158 ASP cc_start: 0.7091 (t0) cc_final: 0.6608 (t0) REVERT: M 341 ILE cc_start: 0.7846 (tp) cc_final: 0.7571 (tp) REVERT: M 476 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7830 (mt-10) REVERT: M 485 MET cc_start: 0.7735 (mmm) cc_final: 0.7364 (mmp) REVERT: M 505 HIS cc_start: 0.6149 (t70) cc_final: 0.5438 (t70) REVERT: N 71 HIS cc_start: 0.6224 (OUTLIER) cc_final: 0.5505 (m-70) REVERT: N 79 LYS cc_start: 0.8488 (pttt) cc_final: 0.8187 (ptpt) REVERT: N 124 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7952 (tm-30) REVERT: N 376 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7274 (pp) REVERT: N 503 GLN cc_start: 0.8839 (tp40) cc_final: 0.7832 (tm-30) REVERT: O 65 ILE cc_start: 0.8924 (pt) cc_final: 0.8639 (pt) REVERT: O 168 ILE cc_start: 0.5357 (OUTLIER) cc_final: 0.5138 (pt) REVERT: O 382 MET cc_start: 0.3011 (OUTLIER) cc_final: 0.2601 (mpp) REVERT: O 455 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7472 (p90) REVERT: O 494 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7068 (mm-30) REVERT: O 499 ARG cc_start: 0.6502 (ttt90) cc_final: 0.6258 (ttt90) REVERT: P 75 GLU cc_start: 0.8105 (tp30) cc_final: 0.7743 (tp30) REVERT: P 84 LYS cc_start: 0.7915 (tmtt) cc_final: 0.7097 (ttmt) REVERT: P 224 LYS cc_start: 0.6677 (pttm) cc_final: 0.6282 (ptmm) REVERT: P 266 MET cc_start: 0.6296 (mmp) cc_final: 0.5653 (mmp) REVERT: P 272 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: P 344 MET cc_start: 0.4234 (mmp) cc_final: 0.3547 (mmp) REVERT: P 389 GLU cc_start: 0.8883 (tp30) cc_final: 0.8174 (tp30) REVERT: P 480 LEU cc_start: 0.8630 (tt) cc_final: 0.8343 (tp) REVERT: P 521 VAL cc_start: 0.9332 (t) cc_final: 0.9124 (m) outliers start: 259 outliers final: 184 residues processed: 1526 average time/residue: 0.5997 time to fit residues: 1606.4701 Evaluate side-chains 1499 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1297 time to evaluate : 5.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 1 residue 89 GLU Chi-restraints excluded: chain 1 residue 94 LEU Chi-restraints excluded: chain 3 residue 77 GLN Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 77 HIS Chi-restraints excluded: chain 5 residue 102 PHE Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 176 LYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 511 ILE Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 345 CYS Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 382 MET Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain G residue 516 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 468 TYR Chi-restraints excluded: chain H residue 471 HIS Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 23 MET Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 436 LEU Chi-restraints excluded: chain I residue 508 ILE Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 399 GLN Chi-restraints excluded: chain J residue 521 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 400 ASN Chi-restraints excluded: chain K residue 408 VAL Chi-restraints excluded: chain K residue 434 GLN Chi-restraints excluded: chain K residue 459 THR Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 108 SER Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 131 THR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 465 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain L residue 535 VAL Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 406 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 491 ILE Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain M residue 527 ILE Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 71 HIS Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 176 ILE Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 437 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 471 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain N residue 508 CYS Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 168 ILE Chi-restraints excluded: chain O residue 193 LYS Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 301 GLN Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 382 MET Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 455 PHE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 468 TYR Chi-restraints excluded: chain P residue 470 VAL Chi-restraints excluded: chain P residue 499 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 803 optimal weight: 0.7980 chunk 93 optimal weight: 30.0000 chunk 474 optimal weight: 0.2980 chunk 608 optimal weight: 0.9990 chunk 471 optimal weight: 5.9990 chunk 701 optimal weight: 1.9990 chunk 465 optimal weight: 10.0000 chunk 829 optimal weight: 20.0000 chunk 519 optimal weight: 0.9990 chunk 505 optimal weight: 0.9980 chunk 383 optimal weight: 6.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 168 GLN ** 4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 109 GLN ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 HIS ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 487 ASN H 93 GLN ** I 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 477 ASN ** J 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN L 301 GLN M 122 GLN N 71 HIS O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 102 ASN P 303 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 67779 Z= 0.203 Angle : 0.733 15.219 91441 Z= 0.361 Chirality : 0.045 0.332 10955 Planarity : 0.004 0.063 11721 Dihedral : 5.906 135.142 9295 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.38 % Favored : 94.60 % Rotamer: Outliers : 3.14 % Allowed : 21.49 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.99 (0.09), residues: 8683 helix: 0.38 (0.07), residues: 4580 sheet: -1.85 (0.20), residues: 649 loop : -1.80 (0.10), residues: 3454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 435 HIS 0.015 0.001 HIS N 71 PHE 0.044 0.002 PHE J 179 TYR 0.024 0.002 TYR K 437 ARG 0.012 0.000 ARG F 396 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1624 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1394 time to evaluate : 6.092 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: 1 89 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: 2 62 LYS cc_start: 0.6193 (ttpt) cc_final: 0.5436 (pttp) REVERT: 3 63 MET cc_start: 0.2617 (mmm) cc_final: 0.1876 (mmt) REVERT: 3 106 LEU cc_start: 0.8370 (mt) cc_final: 0.6953 (pp) REVERT: 6 54 ASN cc_start: 0.4177 (m-40) cc_final: 0.3681 (m-40) REVERT: A 167 PHE cc_start: 0.8808 (t80) cc_final: 0.8592 (t80) REVERT: A 171 MET cc_start: 0.8221 (mtt) cc_final: 0.7336 (tpt) REVERT: A 426 TYR cc_start: 0.8665 (t80) cc_final: 0.8350 (t80) REVERT: A 440 GLU cc_start: 0.8296 (tp30) cc_final: 0.7973 (tp30) REVERT: B 48 MET cc_start: 0.8652 (ttp) cc_final: 0.8273 (ttp) REVERT: B 52 LEU cc_start: 0.8932 (mm) cc_final: 0.8727 (mm) REVERT: B 114 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7538 (tm-30) REVERT: B 138 ARG cc_start: 0.8076 (tmm-80) cc_final: 0.7849 (tmm-80) REVERT: B 495 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7484 (mm-30) REVERT: B 504 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8592 (tp) REVERT: C 38 ARG cc_start: 0.8431 (ttm110) cc_final: 0.8154 (ttm110) REVERT: C 40 CYS cc_start: 0.7981 (m) cc_final: 0.7658 (m) REVERT: C 152 MET cc_start: 0.6842 (mpp) cc_final: 0.6565 (mpp) REVERT: C 188 ASN cc_start: 0.6445 (t0) cc_final: 0.5991 (t0) REVERT: C 453 GLN cc_start: 0.8498 (tm-30) cc_final: 0.7825 (tm-30) REVERT: C 476 GLU cc_start: 0.7530 (mp0) cc_final: 0.7084 (mp0) REVERT: C 504 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7349 (tm-30) REVERT: D 533 ASP cc_start: 0.6929 (m-30) cc_final: 0.6519 (m-30) REVERT: E 79 SER cc_start: 0.9004 (t) cc_final: 0.8449 (p) REVERT: E 208 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6471 (pp) REVERT: E 436 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7641 (tm-30) REVERT: E 444 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7145 (mt-10) REVERT: E 446 TYR cc_start: 0.8266 (m-80) cc_final: 0.8040 (m-80) REVERT: F 36 THR cc_start: 0.8202 (p) cc_final: 0.7703 (t) REVERT: F 43 THR cc_start: 0.7679 (p) cc_final: 0.7082 (p) REVERT: F 145 ARG cc_start: 0.7206 (tpt170) cc_final: 0.6335 (tpt-90) REVERT: F 150 ASP cc_start: 0.8659 (m-30) cc_final: 0.8193 (t0) REVERT: F 190 MET cc_start: 0.6090 (pmm) cc_final: 0.5711 (pmm) REVERT: F 195 GLU cc_start: 0.7850 (mp0) cc_final: 0.6930 (mt-10) REVERT: F 381 LYS cc_start: 0.8454 (mmmt) cc_final: 0.7978 (mmmm) REVERT: F 494 VAL cc_start: 0.8700 (t) cc_final: 0.8481 (t) REVERT: G 55 LYS cc_start: 0.8125 (tppt) cc_final: 0.7808 (tptp) REVERT: G 73 HIS cc_start: 0.7732 (t-90) cc_final: 0.7380 (t-90) REVERT: G 185 MET cc_start: 0.4395 (OUTLIER) cc_final: 0.3426 (ppp) REVERT: G 430 LYS cc_start: 0.8425 (ptmt) cc_final: 0.8163 (ttpt) REVERT: G 467 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6327 (ttm170) REVERT: G 514 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8707 (p) REVERT: H 127 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7285 (mm-30) REVERT: H 347 CYS cc_start: 0.6061 (m) cc_final: 0.5660 (p) REVERT: I 36 LEU cc_start: 0.8488 (tp) cc_final: 0.8205 (tp) REVERT: I 127 GLU cc_start: 0.8265 (tp30) cc_final: 0.7853 (tp30) REVERT: I 148 LEU cc_start: 0.7050 (mp) cc_final: 0.6580 (tt) REVERT: I 225 MET cc_start: 0.1200 (OUTLIER) cc_final: 0.0821 (ptt) REVERT: J 72 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8505 (mmmm) REVERT: J 353 MET cc_start: 0.5656 (mmm) cc_final: 0.5157 (mmm) REVERT: K 20 ARG cc_start: 0.6674 (tpp-160) cc_final: 0.5950 (tpt170) REVERT: K 305 MET cc_start: 0.6405 (mmp) cc_final: 0.3331 (pmm) REVERT: K 492 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: L 115 SER cc_start: 0.8427 (m) cc_final: 0.8077 (t) REVERT: L 120 CYS cc_start: 0.7935 (t) cc_final: 0.7518 (t) REVERT: L 299 LEU cc_start: 0.3524 (OUTLIER) cc_final: 0.3300 (pp) REVERT: M 119 GLU cc_start: 0.7740 (tp30) cc_final: 0.7522 (tp30) REVERT: M 132 ARG cc_start: 0.7958 (mmm-85) cc_final: 0.7349 (mmm160) REVERT: M 158 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6366 (t0) REVERT: M 341 ILE cc_start: 0.7857 (tp) cc_final: 0.7567 (tp) REVERT: M 411 ASN cc_start: 0.8438 (m-40) cc_final: 0.8190 (m-40) REVERT: M 443 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7744 (pt) REVERT: M 476 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7868 (mt-10) REVERT: M 485 MET cc_start: 0.7627 (mmm) cc_final: 0.7246 (mmp) REVERT: M 505 HIS cc_start: 0.6082 (t70) cc_final: 0.5305 (t70) REVERT: N 71 HIS cc_start: 0.6116 (t-90) cc_final: 0.5583 (m-70) REVERT: N 79 LYS cc_start: 0.8478 (pttt) cc_final: 0.8179 (ptpt) REVERT: N 124 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7935 (tm-30) REVERT: N 300 PHE cc_start: 0.6300 (m-10) cc_final: 0.5526 (t80) REVERT: N 376 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7169 (pp) REVERT: N 438 GLN cc_start: 0.8705 (tp40) cc_final: 0.8357 (tm-30) REVERT: N 461 GLU cc_start: 0.7572 (tp30) cc_final: 0.6965 (tp30) REVERT: N 503 GLN cc_start: 0.8801 (tp40) cc_final: 0.7784 (tm-30) REVERT: O 65 ILE cc_start: 0.8897 (pt) cc_final: 0.8536 (pt) REVERT: O 145 LYS cc_start: 0.5941 (ptpp) cc_final: 0.5573 (ptmt) REVERT: O 382 MET cc_start: 0.2833 (OUTLIER) cc_final: 0.2437 (mpp) REVERT: O 455 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7328 (p90) REVERT: O 494 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6911 (mm-30) REVERT: O 499 ARG cc_start: 0.6427 (ttt90) cc_final: 0.6145 (ttt90) REVERT: P 75 GLU cc_start: 0.8123 (tp30) cc_final: 0.7831 (tp30) REVERT: P 84 LYS cc_start: 0.7873 (tmtt) cc_final: 0.7023 (ttmt) REVERT: P 224 LYS cc_start: 0.6457 (pttm) cc_final: 0.6134 (ptmm) REVERT: P 266 MET cc_start: 0.6215 (mmp) cc_final: 0.5589 (mmp) REVERT: P 272 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6760 (mt-10) REVERT: P 344 MET cc_start: 0.4199 (mmp) cc_final: 0.3564 (mmp) REVERT: P 389 GLU cc_start: 0.8806 (tp30) cc_final: 0.8099 (tp30) REVERT: P 480 LEU cc_start: 0.8611 (tt) cc_final: 0.8367 (tp) outliers start: 230 outliers final: 170 residues processed: 1529 average time/residue: 0.6113 time to fit residues: 1632.3068 Evaluate side-chains 1502 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1317 time to evaluate : 5.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 1 residue 89 GLU Chi-restraints excluded: chain 3 residue 77 GLN Chi-restraints excluded: chain 3 residue 86 GLU Chi-restraints excluded: chain 4 residue 109 GLN Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 77 HIS Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 382 MET Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 471 HIS Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 31 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 508 ILE Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 399 GLN Chi-restraints excluded: chain J residue 509 GLU Chi-restraints excluded: chain J residue 521 ILE Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 151 MET Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 400 ASN Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 465 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 443 LEU Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 491 ILE Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 521 THR Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain M residue 527 ILE Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 437 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 471 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 288 VAL Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 382 MET Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 455 PHE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 445 PHE Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 468 TYR Chi-restraints excluded: chain P residue 499 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 513 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 495 optimal weight: 7.9990 chunk 249 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 527 optimal weight: 0.9990 chunk 565 optimal weight: 3.9990 chunk 410 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 652 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 35 GLN ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 30 GLN G 487 ASN H 93 GLN ** I 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 67779 Z= 0.217 Angle : 0.746 18.674 91441 Z= 0.368 Chirality : 0.045 0.311 10955 Planarity : 0.004 0.065 11721 Dihedral : 5.807 133.369 9295 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.49 % Favored : 94.48 % Rotamer: Outliers : 3.26 % Allowed : 22.04 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.95 (0.09), residues: 8683 helix: 0.41 (0.07), residues: 4583 sheet: -1.84 (0.20), residues: 659 loop : -1.78 (0.10), residues: 3441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 130 HIS 0.012 0.001 HIS O 390 PHE 0.046 0.002 PHE J 179 TYR 0.026 0.002 TYR K 437 ARG 0.013 0.000 ARG K 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1605 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1366 time to evaluate : 6.067 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: 2 62 LYS cc_start: 0.6176 (ttpt) cc_final: 0.5406 (pttp) REVERT: 2 71 TYR cc_start: 0.5973 (m-80) cc_final: 0.5526 (m-80) REVERT: 3 106 LEU cc_start: 0.8293 (mt) cc_final: 0.6913 (pp) REVERT: 3 110 ASN cc_start: 0.2489 (p0) cc_final: 0.2238 (p0) REVERT: 3 126 TRP cc_start: 0.4573 (p-90) cc_final: 0.4001 (p-90) REVERT: 6 54 ASN cc_start: 0.4132 (m-40) cc_final: 0.3569 (m-40) REVERT: A 167 PHE cc_start: 0.8796 (t80) cc_final: 0.8595 (t80) REVERT: A 171 MET cc_start: 0.8243 (mtt) cc_final: 0.7213 (tpt) REVERT: A 426 TYR cc_start: 0.8686 (t80) cc_final: 0.8392 (t80) REVERT: A 440 GLU cc_start: 0.8331 (tp30) cc_final: 0.8002 (tp30) REVERT: B 48 MET cc_start: 0.8732 (ttp) cc_final: 0.8522 (ttp) REVERT: B 138 ARG cc_start: 0.8095 (tmm-80) cc_final: 0.7867 (tmm-80) REVERT: B 495 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 504 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8550 (tp) REVERT: C 38 ARG cc_start: 0.8420 (ttm110) cc_final: 0.8189 (ttm110) REVERT: C 40 CYS cc_start: 0.8019 (m) cc_final: 0.7673 (m) REVERT: C 132 ASP cc_start: 0.8642 (m-30) cc_final: 0.8127 (t0) REVERT: C 188 ASN cc_start: 0.6420 (t0) cc_final: 0.5934 (t0) REVERT: C 453 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8026 (tm-30) REVERT: C 476 GLU cc_start: 0.7494 (mp0) cc_final: 0.7046 (mp0) REVERT: C 504 GLN cc_start: 0.7660 (tm-30) cc_final: 0.7343 (tm-30) REVERT: D 533 ASP cc_start: 0.6841 (m-30) cc_final: 0.6636 (m-30) REVERT: E 199 MET cc_start: 0.4420 (tmm) cc_final: 0.4112 (tmm) REVERT: E 208 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6516 (pp) REVERT: E 436 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7726 (tm-30) REVERT: E 444 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7117 (mt-10) REVERT: F 36 THR cc_start: 0.8155 (p) cc_final: 0.7682 (t) REVERT: F 43 THR cc_start: 0.7695 (p) cc_final: 0.7124 (p) REVERT: F 44 MET cc_start: 0.6959 (tpp) cc_final: 0.6736 (tpp) REVERT: F 145 ARG cc_start: 0.7062 (tpt170) cc_final: 0.6348 (tpt-90) REVERT: F 150 ASP cc_start: 0.8673 (m-30) cc_final: 0.8216 (t0) REVERT: F 190 MET cc_start: 0.6145 (pmm) cc_final: 0.5832 (pmm) REVERT: F 195 GLU cc_start: 0.7954 (mp0) cc_final: 0.7041 (mt-10) REVERT: F 342 ASP cc_start: 0.6644 (p0) cc_final: 0.6400 (p0) REVERT: F 381 LYS cc_start: 0.8433 (mmmt) cc_final: 0.7940 (mmmm) REVERT: F 494 VAL cc_start: 0.8723 (t) cc_final: 0.8515 (t) REVERT: F 522 MET cc_start: 0.7909 (mmm) cc_final: 0.7652 (mmp) REVERT: G 55 LYS cc_start: 0.8120 (tppt) cc_final: 0.7809 (tptp) REVERT: G 73 HIS cc_start: 0.7704 (t-90) cc_final: 0.7452 (t-90) REVERT: G 185 MET cc_start: 0.4313 (OUTLIER) cc_final: 0.3488 (ppp) REVERT: G 430 LYS cc_start: 0.8427 (ptmt) cc_final: 0.8186 (ttpt) REVERT: G 467 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6221 (ttm170) REVERT: G 468 HIS cc_start: 0.7558 (OUTLIER) cc_final: 0.6910 (t-170) REVERT: G 477 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7910 (p) REVERT: H 88 MET cc_start: 0.7431 (mtm) cc_final: 0.7090 (mtm) REVERT: H 127 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7175 (mm-30) REVERT: H 347 CYS cc_start: 0.6035 (m) cc_final: 0.5593 (p) REVERT: I 36 LEU cc_start: 0.8471 (tp) cc_final: 0.8178 (tp) REVERT: I 43 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6358 (mmmm) REVERT: I 148 LEU cc_start: 0.7034 (mp) cc_final: 0.6764 (tt) REVERT: I 225 MET cc_start: 0.1157 (OUTLIER) cc_final: 0.0894 (ptt) REVERT: I 246 MET cc_start: 0.3315 (mmt) cc_final: 0.0849 (mtm) REVERT: J 72 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8465 (mmmm) REVERT: J 112 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7375 (mm-30) REVERT: J 353 MET cc_start: 0.5604 (mmm) cc_final: 0.5198 (mmm) REVERT: J 441 LYS cc_start: 0.8646 (tttp) cc_final: 0.8215 (tttp) REVERT: K 20 ARG cc_start: 0.6607 (tpp-160) cc_final: 0.5983 (tpt170) REVERT: K 305 MET cc_start: 0.6288 (mmp) cc_final: 0.3288 (pmm) REVERT: L 115 SER cc_start: 0.8446 (m) cc_final: 0.8134 (t) REVERT: L 120 CYS cc_start: 0.7688 (t) cc_final: 0.7349 (t) REVERT: M 119 GLU cc_start: 0.7799 (tp30) cc_final: 0.7516 (tp30) REVERT: M 132 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7326 (mmm160) REVERT: M 158 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6426 (t0) REVERT: M 341 ILE cc_start: 0.7841 (tp) cc_final: 0.7640 (tp) REVERT: M 411 ASN cc_start: 0.8451 (m-40) cc_final: 0.8191 (m-40) REVERT: M 476 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7894 (mt-10) REVERT: M 485 MET cc_start: 0.7629 (mmm) cc_final: 0.7239 (mmp) REVERT: M 505 HIS cc_start: 0.6206 (t70) cc_final: 0.5400 (t70) REVERT: N 71 HIS cc_start: 0.6289 (t-90) cc_final: 0.5650 (m-70) REVERT: N 75 SER cc_start: 0.8619 (m) cc_final: 0.7996 (p) REVERT: N 79 LYS cc_start: 0.8464 (pttt) cc_final: 0.8185 (ptpt) REVERT: N 124 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7946 (tm-30) REVERT: N 300 PHE cc_start: 0.6253 (m-10) cc_final: 0.5533 (t80) REVERT: N 376 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7198 (pp) REVERT: N 438 GLN cc_start: 0.8712 (tp40) cc_final: 0.8341 (tm-30) REVERT: N 503 GLN cc_start: 0.8793 (tp40) cc_final: 0.7815 (tm-30) REVERT: N 523 ARG cc_start: 0.5968 (mtt180) cc_final: 0.5680 (mtt180) REVERT: O 65 ILE cc_start: 0.8898 (pt) cc_final: 0.8607 (pt) REVERT: O 145 LYS cc_start: 0.5900 (ptpp) cc_final: 0.5520 (ptmt) REVERT: O 382 MET cc_start: 0.2634 (OUTLIER) cc_final: 0.2373 (mpp) REVERT: O 455 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7352 (p90) REVERT: O 494 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6884 (mm-30) REVERT: O 499 ARG cc_start: 0.6464 (ttt90) cc_final: 0.6183 (ttt90) REVERT: P 75 GLU cc_start: 0.8013 (tp30) cc_final: 0.7653 (tp30) REVERT: P 84 LYS cc_start: 0.7855 (tmtt) cc_final: 0.6999 (ttmt) REVERT: P 266 MET cc_start: 0.6238 (mmp) cc_final: 0.5597 (mmp) REVERT: P 272 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6846 (mt-10) REVERT: P 311 MET cc_start: 0.5302 (mpp) cc_final: 0.4843 (mpp) REVERT: P 344 MET cc_start: 0.4242 (mmp) cc_final: 0.3565 (mmp) REVERT: P 389 GLU cc_start: 0.8801 (tp30) cc_final: 0.8052 (tp30) REVERT: P 480 LEU cc_start: 0.8700 (tt) cc_final: 0.8421 (tp) outliers start: 239 outliers final: 180 residues processed: 1514 average time/residue: 0.6267 time to fit residues: 1675.9198 Evaluate side-chains 1504 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1312 time to evaluate : 5.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 53 THR Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 3 residue 77 GLN Chi-restraints excluded: chain 3 residue 86 GLU Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 77 HIS Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 382 MET Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 471 HIS Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 508 ILE Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 399 GLN Chi-restraints excluded: chain J residue 415 MET Chi-restraints excluded: chain J residue 521 ILE Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 400 ASN Chi-restraints excluded: chain K residue 459 THR Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain K residue 522 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 465 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 158 ASP Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain M residue 527 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 437 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 471 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain N residue 508 CYS Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 193 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 288 VAL Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 382 MET Chi-restraints excluded: chain O residue 396 VAL Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 455 PHE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 512 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 445 PHE Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 468 TYR Chi-restraints excluded: chain P residue 499 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 754 optimal weight: 0.8980 chunk 795 optimal weight: 3.9990 chunk 725 optimal weight: 5.9990 chunk 773 optimal weight: 0.9980 chunk 794 optimal weight: 6.9990 chunk 465 optimal weight: 4.9990 chunk 336 optimal weight: 0.0070 chunk 607 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 698 optimal weight: 0.9990 chunk 731 optimal weight: 5.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 49 ASN ** 4 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 109 GLN ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 113 GLN ** 6 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** I 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 122 GLN ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 67779 Z= 0.227 Angle : 0.763 16.936 91441 Z= 0.375 Chirality : 0.045 0.323 10955 Planarity : 0.004 0.066 11721 Dihedral : 5.749 134.470 9295 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 3.14 % Allowed : 22.47 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.94 (0.09), residues: 8683 helix: 0.42 (0.07), residues: 4591 sheet: -1.76 (0.20), residues: 645 loop : -1.80 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 496 HIS 0.009 0.001 HIS C 470 PHE 0.060 0.002 PHE 1 68 TYR 0.025 0.001 TYR O 302 ARG 0.013 0.000 ARG G 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1569 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1339 time to evaluate : 5.945 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: 2 62 LYS cc_start: 0.6170 (ttpt) cc_final: 0.5401 (pttp) REVERT: 2 71 TYR cc_start: 0.6100 (m-80) cc_final: 0.5682 (m-80) REVERT: 3 63 MET cc_start: 0.2448 (mmm) cc_final: 0.1876 (mmt) REVERT: 3 126 TRP cc_start: 0.4574 (p-90) cc_final: 0.4034 (p-90) REVERT: 6 54 ASN cc_start: 0.4390 (m-40) cc_final: 0.3820 (m-40) REVERT: A 171 MET cc_start: 0.8257 (mtt) cc_final: 0.7219 (tpt) REVERT: A 440 GLU cc_start: 0.8332 (tp30) cc_final: 0.8010 (tp30) REVERT: B 48 MET cc_start: 0.8786 (ttp) cc_final: 0.8532 (ttp) REVERT: B 138 ARG cc_start: 0.8123 (tmm-80) cc_final: 0.7880 (tmm-80) REVERT: B 495 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7502 (mm-30) REVERT: B 504 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8564 (tp) REVERT: C 38 ARG cc_start: 0.8448 (ttm110) cc_final: 0.8212 (ttm110) REVERT: C 40 CYS cc_start: 0.8004 (m) cc_final: 0.7662 (m) REVERT: C 132 ASP cc_start: 0.8625 (m-30) cc_final: 0.8175 (t0) REVERT: C 188 ASN cc_start: 0.6369 (t0) cc_final: 0.5893 (t0) REVERT: C 395 MET cc_start: 0.7457 (ptp) cc_final: 0.7211 (mtm) REVERT: C 415 GLU cc_start: 0.8717 (mp0) cc_final: 0.8041 (mp0) REVERT: C 453 GLN cc_start: 0.8513 (tm-30) cc_final: 0.8022 (tm-30) REVERT: C 476 GLU cc_start: 0.7537 (mp0) cc_final: 0.7103 (mp0) REVERT: C 504 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7291 (tm-30) REVERT: D 532 ILE cc_start: 0.8735 (mm) cc_final: 0.8506 (mt) REVERT: D 533 ASP cc_start: 0.6885 (m-30) cc_final: 0.6668 (m-30) REVERT: E 208 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6604 (pp) REVERT: E 436 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7693 (tm-30) REVERT: E 444 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7216 (mt-10) REVERT: F 36 THR cc_start: 0.8194 (p) cc_final: 0.7733 (t) REVERT: F 43 THR cc_start: 0.7749 (p) cc_final: 0.7174 (p) REVERT: F 44 MET cc_start: 0.7029 (tpp) cc_final: 0.6795 (tpp) REVERT: F 145 ARG cc_start: 0.7115 (tpt170) cc_final: 0.6468 (tpt-90) REVERT: F 150 ASP cc_start: 0.8681 (m-30) cc_final: 0.8221 (t0) REVERT: F 190 MET cc_start: 0.6019 (pmm) cc_final: 0.5721 (pmm) REVERT: F 195 GLU cc_start: 0.7935 (mp0) cc_final: 0.7078 (mt-10) REVERT: F 342 ASP cc_start: 0.6657 (p0) cc_final: 0.6408 (p0) REVERT: F 381 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7970 (mmmm) REVERT: F 418 MET cc_start: 0.7974 (ptm) cc_final: 0.7663 (mtm) REVERT: F 494 VAL cc_start: 0.8742 (t) cc_final: 0.8538 (t) REVERT: G 55 LYS cc_start: 0.8138 (tppt) cc_final: 0.7828 (tptp) REVERT: G 73 HIS cc_start: 0.7781 (t-90) cc_final: 0.7418 (t-90) REVERT: G 467 ARG cc_start: 0.6820 (OUTLIER) cc_final: 0.6285 (ttm170) REVERT: G 468 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6939 (t-170) REVERT: G 477 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7759 (p) REVERT: G 514 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8701 (p) REVERT: H 88 MET cc_start: 0.7442 (mtm) cc_final: 0.7160 (mtm) REVERT: H 127 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7202 (mm-30) REVERT: H 347 CYS cc_start: 0.5967 (m) cc_final: 0.5607 (p) REVERT: I 36 LEU cc_start: 0.8458 (tp) cc_final: 0.8186 (tp) REVERT: I 127 GLU cc_start: 0.8294 (tp30) cc_final: 0.7888 (tp30) REVERT: I 148 LEU cc_start: 0.7102 (mp) cc_final: 0.6847 (tt) REVERT: J 72 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8524 (mmmm) REVERT: J 353 MET cc_start: 0.5766 (mmm) cc_final: 0.5421 (mmm) REVERT: J 365 VAL cc_start: -0.1438 (OUTLIER) cc_final: -0.1943 (t) REVERT: J 415 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7641 (tpt) REVERT: K 20 ARG cc_start: 0.6598 (tpp-160) cc_final: 0.5989 (tpt170) REVERT: K 305 MET cc_start: 0.6124 (mmp) cc_final: 0.3164 (pmm) REVERT: K 492 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: L 115 SER cc_start: 0.8468 (m) cc_final: 0.8155 (t) REVERT: L 120 CYS cc_start: 0.7706 (t) cc_final: 0.7384 (t) REVERT: M 132 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7366 (mmm160) REVERT: M 341 ILE cc_start: 0.7825 (tp) cc_final: 0.7599 (tp) REVERT: M 411 ASN cc_start: 0.8430 (m-40) cc_final: 0.8220 (m-40) REVERT: M 476 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7799 (mt-10) REVERT: M 485 MET cc_start: 0.7631 (mmm) cc_final: 0.7235 (mmp) REVERT: M 505 HIS cc_start: 0.6233 (t70) cc_final: 0.5462 (t70) REVERT: N 71 HIS cc_start: 0.6254 (t-90) cc_final: 0.5638 (m-70) REVERT: N 75 SER cc_start: 0.8630 (m) cc_final: 0.8006 (p) REVERT: N 79 LYS cc_start: 0.8466 (pttt) cc_final: 0.8177 (ptpt) REVERT: N 124 GLU cc_start: 0.8281 (tm-30) cc_final: 0.7942 (tm-30) REVERT: N 300 PHE cc_start: 0.6196 (m-10) cc_final: 0.5541 (t80) REVERT: N 376 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7138 (pp) REVERT: N 438 GLN cc_start: 0.8691 (tp40) cc_final: 0.8332 (tm-30) REVERT: N 503 GLN cc_start: 0.8786 (tp40) cc_final: 0.7818 (tm-30) REVERT: N 523 ARG cc_start: 0.5947 (mtt180) cc_final: 0.5634 (mtt180) REVERT: O 38 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8714 (m) REVERT: O 65 ILE cc_start: 0.8920 (pt) cc_final: 0.8604 (pt) REVERT: O 145 LYS cc_start: 0.5940 (ptpp) cc_final: 0.5512 (ptmt) REVERT: O 360 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.5585 (m-80) REVERT: O 455 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7393 (p90) REVERT: O 494 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6923 (mm-30) REVERT: O 499 ARG cc_start: 0.6458 (ttt90) cc_final: 0.6185 (ttt90) REVERT: P 84 LYS cc_start: 0.7864 (tmtt) cc_final: 0.7431 (tptp) REVERT: P 266 MET cc_start: 0.6231 (mmp) cc_final: 0.5559 (mmp) REVERT: P 272 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: P 344 MET cc_start: 0.4237 (mmp) cc_final: 0.3571 (mmp) REVERT: P 389 GLU cc_start: 0.8755 (tp30) cc_final: 0.8004 (tp30) REVERT: P 480 LEU cc_start: 0.8701 (tt) cc_final: 0.8427 (tp) outliers start: 230 outliers final: 190 residues processed: 1475 average time/residue: 0.6112 time to fit residues: 1582.7144 Evaluate side-chains 1499 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1295 time to evaluate : 6.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 3 residue 77 GLN Chi-restraints excluded: chain 3 residue 86 GLU Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 77 HIS Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 129 HIS Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain F residue 461 GLU Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 514 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 471 HIS Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain H residue 521 VAL Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 508 ILE Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 399 GLN Chi-restraints excluded: chain J residue 415 MET Chi-restraints excluded: chain J residue 521 ILE Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 459 THR Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 465 LEU Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 47 THR Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 521 THR Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain M residue 527 ILE Chi-restraints excluded: chain N residue 73 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 437 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 471 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain N residue 508 CYS Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 193 LYS Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 288 VAL Chi-restraints excluded: chain O residue 297 ASP Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 360 PHE Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 393 ILE Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 455 PHE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 512 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 272 GLU Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 372 ILE Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 445 PHE Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 468 TYR Chi-restraints excluded: chain P residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 770 optimal weight: 0.5980 chunk 507 optimal weight: 0.8980 chunk 817 optimal weight: 9.9990 chunk 499 optimal weight: 1.9990 chunk 387 optimal weight: 5.9990 chunk 568 optimal weight: 0.7980 chunk 857 optimal weight: 1.9990 chunk 789 optimal weight: 6.9990 chunk 683 optimal weight: 30.0000 chunk 70 optimal weight: 0.8980 chunk 527 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 4 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 93 GLN ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 HIS ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 67779 Z= 0.214 Angle : 0.783 17.372 91441 Z= 0.383 Chirality : 0.046 0.313 10955 Planarity : 0.004 0.084 11721 Dihedral : 5.703 135.562 9295 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.46 % Favored : 94.52 % Rotamer: Outliers : 2.99 % Allowed : 22.95 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.95 (0.09), residues: 8683 helix: 0.41 (0.07), residues: 4587 sheet: -1.74 (0.20), residues: 634 loop : -1.80 (0.10), residues: 3462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 130 HIS 0.011 0.001 HIS O 390 PHE 0.043 0.002 PHE J 179 TYR 0.056 0.002 TYR O 302 ARG 0.015 0.000 ARG G 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17366 Ramachandran restraints generated. 8683 Oldfield, 0 Emsley, 8683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1578 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 1359 time to evaluate : 6.301 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: 1 117 MET cc_start: 0.5551 (mmp) cc_final: 0.4680 (mmp) REVERT: 2 62 LYS cc_start: 0.6157 (ttpt) cc_final: 0.5408 (pttp) REVERT: 2 71 TYR cc_start: 0.6267 (m-80) cc_final: 0.5802 (m-80) REVERT: 3 63 MET cc_start: 0.2435 (mmm) cc_final: 0.1858 (mmt) REVERT: 3 126 TRP cc_start: 0.4521 (p-90) cc_final: 0.3952 (p-90) REVERT: 4 95 GLN cc_start: 0.7076 (pp30) cc_final: 0.6792 (tp40) REVERT: 6 54 ASN cc_start: 0.4573 (m-40) cc_final: 0.4008 (m110) REVERT: A 103 ASN cc_start: 0.6442 (m-40) cc_final: 0.5963 (m110) REVERT: A 426 TYR cc_start: 0.8656 (t80) cc_final: 0.8368 (t80) REVERT: B 48 MET cc_start: 0.8758 (ttp) cc_final: 0.8527 (ttp) REVERT: B 138 ARG cc_start: 0.8109 (tmm-80) cc_final: 0.7873 (tmm-80) REVERT: B 249 ILE cc_start: 0.7184 (mm) cc_final: 0.6948 (mt) REVERT: B 495 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7360 (mm-30) REVERT: B 504 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8565 (tp) REVERT: C 40 CYS cc_start: 0.7927 (m) cc_final: 0.7619 (m) REVERT: C 132 ASP cc_start: 0.8610 (m-30) cc_final: 0.8162 (t0) REVERT: C 151 MET cc_start: 0.6076 (mmt) cc_final: 0.5471 (mpp) REVERT: C 188 ASN cc_start: 0.6385 (t0) cc_final: 0.5931 (t0) REVERT: C 395 MET cc_start: 0.7485 (ptp) cc_final: 0.7250 (mtm) REVERT: C 453 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 476 GLU cc_start: 0.7581 (mp0) cc_final: 0.7106 (mp0) REVERT: C 504 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7273 (tm-30) REVERT: D 532 ILE cc_start: 0.8740 (mm) cc_final: 0.8491 (mt) REVERT: D 533 ASP cc_start: 0.6922 (m-30) cc_final: 0.6703 (m-30) REVERT: E 199 MET cc_start: 0.4353 (tmm) cc_final: 0.4119 (tmm) REVERT: E 436 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7593 (tm-30) REVERT: E 444 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7315 (mt-10) REVERT: F 36 THR cc_start: 0.8197 (p) cc_final: 0.7977 (p) REVERT: F 43 THR cc_start: 0.7745 (p) cc_final: 0.7467 (p) REVERT: F 44 MET cc_start: 0.7059 (tpp) cc_final: 0.6783 (tpp) REVERT: F 145 ARG cc_start: 0.7118 (tpt170) cc_final: 0.6523 (tpt-90) REVERT: F 150 ASP cc_start: 0.8654 (m-30) cc_final: 0.8242 (t0) REVERT: F 195 GLU cc_start: 0.7924 (mp0) cc_final: 0.6985 (mt-10) REVERT: F 342 ASP cc_start: 0.6626 (p0) cc_final: 0.6382 (p0) REVERT: F 381 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7943 (mmmm) REVERT: F 520 GLU cc_start: 0.6278 (mm-30) cc_final: 0.5850 (mm-30) REVERT: G 55 LYS cc_start: 0.8179 (tppt) cc_final: 0.7846 (tptp) REVERT: G 73 HIS cc_start: 0.7770 (t-90) cc_final: 0.7415 (t-90) REVERT: G 308 MET cc_start: 0.4253 (tpp) cc_final: 0.4015 (tpp) REVERT: G 467 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6398 (ttm170) REVERT: G 468 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6845 (t-170) REVERT: H 127 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7209 (mm-30) REVERT: H 159 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5829 (tt0) REVERT: H 347 CYS cc_start: 0.6011 (m) cc_final: 0.5732 (p) REVERT: I 36 LEU cc_start: 0.8413 (tp) cc_final: 0.8130 (tp) REVERT: I 148 LEU cc_start: 0.7104 (mp) cc_final: 0.6828 (tt) REVERT: J 72 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8491 (mmmm) REVERT: J 365 VAL cc_start: -0.1272 (OUTLIER) cc_final: -0.1757 (t) REVERT: J 415 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7637 (mmm) REVERT: J 441 LYS cc_start: 0.8594 (tttm) cc_final: 0.7734 (mtpp) REVERT: K 20 ARG cc_start: 0.6543 (tpp-160) cc_final: 0.5935 (tpt170) REVERT: K 305 MET cc_start: 0.6188 (mmp) cc_final: 0.3302 (pmm) REVERT: K 400 ASN cc_start: 0.6930 (p0) cc_final: 0.6639 (p0) REVERT: L 115 SER cc_start: 0.8405 (m) cc_final: 0.8135 (t) REVERT: L 120 CYS cc_start: 0.7663 (t) cc_final: 0.7306 (t) REVERT: L 150 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6738 (t0) REVERT: L 299 LEU cc_start: 0.3350 (OUTLIER) cc_final: 0.3043 (pp) REVERT: L 320 MET cc_start: 0.3682 (OUTLIER) cc_final: 0.2473 (ppp) REVERT: M 89 LYS cc_start: 0.8645 (tppt) cc_final: 0.8318 (ttpt) REVERT: M 132 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7304 (mmm160) REVERT: M 341 ILE cc_start: 0.7762 (tp) cc_final: 0.7238 (tp) REVERT: M 411 ASN cc_start: 0.8439 (m-40) cc_final: 0.8213 (m-40) REVERT: M 476 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7620 (mt-10) REVERT: M 485 MET cc_start: 0.7626 (mmm) cc_final: 0.7233 (mmp) REVERT: M 505 HIS cc_start: 0.6220 (t70) cc_final: 0.5448 (t70) REVERT: N 44 MET cc_start: 0.7852 (ptp) cc_final: 0.7650 (ptp) REVERT: N 46 MET cc_start: 0.7942 (ptp) cc_final: 0.7594 (ptp) REVERT: N 66 GLU cc_start: 0.7434 (pt0) cc_final: 0.7168 (pt0) REVERT: N 71 HIS cc_start: 0.6218 (t-90) cc_final: 0.5622 (m-70) REVERT: N 75 SER cc_start: 0.8613 (m) cc_final: 0.7980 (p) REVERT: N 79 LYS cc_start: 0.8450 (pttt) cc_final: 0.8152 (ptpt) REVERT: N 124 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7935 (tm-30) REVERT: N 300 PHE cc_start: 0.6129 (m-10) cc_final: 0.5522 (t80) REVERT: N 376 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7098 (pp) REVERT: N 438 GLN cc_start: 0.8663 (tp40) cc_final: 0.8332 (tm-30) REVERT: N 503 GLN cc_start: 0.8766 (tp40) cc_final: 0.7814 (tm-30) REVERT: N 523 ARG cc_start: 0.5989 (mtt180) cc_final: 0.5685 (mtt180) REVERT: O 38 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8996 (m) REVERT: O 65 ILE cc_start: 0.8887 (pt) cc_final: 0.8600 (pt) REVERT: O 145 LYS cc_start: 0.5812 (ptpp) cc_final: 0.5406 (ptmt) REVERT: O 455 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7374 (p90) REVERT: O 494 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6811 (mm-30) REVERT: O 499 ARG cc_start: 0.6416 (ttt90) cc_final: 0.6132 (ttt90) REVERT: P 84 LYS cc_start: 0.7805 (tmtt) cc_final: 0.7398 (tptp) REVERT: P 266 MET cc_start: 0.6239 (mmp) cc_final: 0.5597 (mmp) REVERT: P 344 MET cc_start: 0.4193 (mmp) cc_final: 0.3522 (mmp) REVERT: P 389 GLU cc_start: 0.8743 (tp30) cc_final: 0.7963 (tp30) REVERT: P 480 LEU cc_start: 0.8719 (tt) cc_final: 0.8446 (tp) outliers start: 219 outliers final: 176 residues processed: 1496 average time/residue: 0.6055 time to fit residues: 1595.5165 Evaluate side-chains 1488 residues out of total 7335 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1300 time to evaluate : 5.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 LEU Chi-restraints excluded: chain 1 residue 64 VAL Chi-restraints excluded: chain 3 residue 77 GLN Chi-restraints excluded: chain 3 residue 86 GLU Chi-restraints excluded: chain 5 residue 45 GLU Chi-restraints excluded: chain 5 residue 77 HIS Chi-restraints excluded: chain 5 residue 127 MET Chi-restraints excluded: chain 6 residue 46 GLU Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 485 TRP Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 462 VAL Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 TYR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 389 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain D residue 535 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 286 GLU Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 484 GLU Chi-restraints excluded: chain E residue 493 CYS Chi-restraints excluded: chain E residue 527 ILE Chi-restraints excluded: chain E residue 530 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 69 ILE Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 206 LEU Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 395 LEU Chi-restraints excluded: chain F residue 504 LEU Chi-restraints excluded: chain F residue 508 CYS Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 289 VAL Chi-restraints excluded: chain G residue 353 ILE Chi-restraints excluded: chain G residue 382 MET Chi-restraints excluded: chain G residue 390 HIS Chi-restraints excluded: chain G residue 467 ARG Chi-restraints excluded: chain G residue 468 HIS Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 159 GLU Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain H residue 187 CYS Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 471 HIS Chi-restraints excluded: chain H residue 497 ILE Chi-restraints excluded: chain H residue 498 LEU Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 182 THR Chi-restraints excluded: chain I residue 195 VAL Chi-restraints excluded: chain I residue 210 LEU Chi-restraints excluded: chain I residue 408 VAL Chi-restraints excluded: chain I residue 415 VAL Chi-restraints excluded: chain I residue 508 ILE Chi-restraints excluded: chain I residue 527 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 365 VAL Chi-restraints excluded: chain J residue 399 GLN Chi-restraints excluded: chain J residue 415 MET Chi-restraints excluded: chain J residue 521 ILE Chi-restraints excluded: chain K residue 57 ILE Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 278 LEU Chi-restraints excluded: chain K residue 459 THR Chi-restraints excluded: chain K residue 492 GLU Chi-restraints excluded: chain L residue 106 THR Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 117 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 241 VAL Chi-restraints excluded: chain L residue 246 ILE Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 320 MET Chi-restraints excluded: chain L residue 476 THR Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 480 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 500 ILE Chi-restraints excluded: chain L residue 512 LEU Chi-restraints excluded: chain M residue 90 LEU Chi-restraints excluded: chain M residue 106 THR Chi-restraints excluded: chain M residue 138 GLU Chi-restraints excluded: chain M residue 202 ARG Chi-restraints excluded: chain M residue 211 VAL Chi-restraints excluded: chain M residue 353 LEU Chi-restraints excluded: chain M residue 372 LEU Chi-restraints excluded: chain M residue 383 VAL Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 526 MET Chi-restraints excluded: chain M residue 527 ILE Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 168 LEU Chi-restraints excluded: chain N residue 235 VAL Chi-restraints excluded: chain N residue 373 THR Chi-restraints excluded: chain N residue 376 ILE Chi-restraints excluded: chain N residue 383 THR Chi-restraints excluded: chain N residue 402 ILE Chi-restraints excluded: chain N residue 437 VAL Chi-restraints excluded: chain N residue 464 VAL Chi-restraints excluded: chain N residue 471 SER Chi-restraints excluded: chain N residue 479 VAL Chi-restraints excluded: chain N residue 481 LEU Chi-restraints excluded: chain N residue 488 VAL Chi-restraints excluded: chain N residue 508 CYS Chi-restraints excluded: chain O residue 29 CYS Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 105 LEU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain O residue 141 VAL Chi-restraints excluded: chain O residue 193 LYS Chi-restraints excluded: chain O residue 199 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 288 VAL Chi-restraints excluded: chain O residue 352 GLN Chi-restraints excluded: chain O residue 359 ASN Chi-restraints excluded: chain O residue 373 ILE Chi-restraints excluded: chain O residue 374 LEU Chi-restraints excluded: chain O residue 393 ILE Chi-restraints excluded: chain O residue 396 VAL Chi-restraints excluded: chain O residue 427 ILE Chi-restraints excluded: chain O residue 442 LEU Chi-restraints excluded: chain O residue 455 PHE Chi-restraints excluded: chain O residue 479 ILE Chi-restraints excluded: chain O residue 512 LEU Chi-restraints excluded: chain P residue 78 VAL Chi-restraints excluded: chain P residue 86 ILE Chi-restraints excluded: chain P residue 101 THR Chi-restraints excluded: chain P residue 102 ASN Chi-restraints excluded: chain P residue 217 VAL Chi-restraints excluded: chain P residue 241 VAL Chi-restraints excluded: chain P residue 362 VAL Chi-restraints excluded: chain P residue 409 VAL Chi-restraints excluded: chain P residue 445 PHE Chi-restraints excluded: chain P residue 448 ILE Chi-restraints excluded: chain P residue 464 ILE Chi-restraints excluded: chain P residue 468 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 861 random chunks: chunk 418 optimal weight: 0.8980 chunk 542 optimal weight: 0.9990 chunk 727 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 629 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 684 optimal weight: 0.0670 chunk 286 optimal weight: 1.9990 chunk 702 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 ASN L 250 GLN L 301 GLN M 122 GLN ** O 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 303 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.184587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.155772 restraints weight = 152804.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.155421 restraints weight = 107519.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.156328 restraints weight = 72739.095| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 67779 Z= 0.207 Angle : 0.784 17.021 91441 Z= 0.384 Chirality : 0.046 0.331 10955 Planarity : 0.004 0.066 11721 Dihedral : 5.627 135.200 9295 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 2.80 % Allowed : 23.40 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.09), residues: 8683 helix: 0.44 (0.08), residues: 4581 sheet: -1.62 (0.21), residues: 614 loop : -1.83 (0.10), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 130 HIS 0.010 0.001 HIS C 470 PHE 0.053 0.002 PHE 1 68 TYR 0.056 0.002 TYR O 302 ARG 0.011 0.000 ARG K 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22096.00 seconds wall clock time: 380 minutes 46.91 seconds (22846.91 seconds total)