Starting phenix.real_space_refine on Sun May 25 22:25:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yb6_39110/05_2025/8yb6_39110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yb6_39110/05_2025/8yb6_39110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yb6_39110/05_2025/8yb6_39110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yb6_39110/05_2025/8yb6_39110.map" model { file = "/net/cci-nas-00/data/ceres_data/8yb6_39110/05_2025/8yb6_39110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yb6_39110/05_2025/8yb6_39110.cif" } resolution = 3.06 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= -0.000 sd= 0.080 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 115 5.16 5 C 17387 2.51 5 N 4884 2.21 5 O 5310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27758 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2768 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2166 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 20, 'TRANS': 246} Chain: "C" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1303 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna2p': 25, 'rna3p': 35} Chain: "D" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2897 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain: "E" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2882 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain: "F" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2911 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain: "G" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2935 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain: "H" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2935 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain: "I" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2072 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 2 Chain: "J" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 28, 'TRANS': 414} Chain: "K" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1356 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2101 SG CYS A 298 41.464 47.449 71.635 1.00 53.53 S ATOM 2122 SG CYS A 301 40.017 49.331 68.641 1.00 54.72 S ATOM 2338 SG CYS A 329 43.654 49.799 69.543 1.00 62.09 S ATOM 2363 SG CYS A 332 40.965 51.236 71.750 1.00 63.65 S ATOM 23999 SG CYS J 215 61.978 39.812 166.800 1.00 87.93 S ATOM 24019 SG CYS J 218 62.860 42.864 164.829 1.00 84.22 S ATOM 24738 SG CYS J 311 59.725 40.770 163.884 1.00 91.10 S ATOM 24756 SG CYS J 314 62.965 39.363 163.113 1.00 94.58 S Time building chain proxies: 15.87, per 1000 atoms: 0.57 Number of scatterers: 27758 At special positions: 0 Unit cell: (113.9, 139.4, 196.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 115 16.00 P 60 15.00 O 5310 8.00 N 4884 7.00 C 17387 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: 6.61 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 301 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 329 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 332 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 298 " pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 311 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 215 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 314 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 218 " Number of angles added : 12 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6268 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 31 sheets defined 38.1% alpha, 16.7% beta 6 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 9.34 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.512A pdb=" N GLY A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.089A pdb=" N LYS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.610A pdb=" N ALA A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.613A pdb=" N ALA A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.836A pdb=" N ARG A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 42 through 48 removed outlier: 3.681A pdb=" N GLU B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.628A pdb=" N CYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 96' Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.961A pdb=" N LYS B 178 " --> pdb=" O TRP B 174 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.881A pdb=" N LYS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.635A pdb=" N ARG D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 removed outlier: 4.218A pdb=" N ALA D 54 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.525A pdb=" N LEU D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.792A pdb=" N TRP D 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS D 79 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LYS D 80 " --> pdb=" O CYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 removed outlier: 4.115A pdb=" N LYS D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.716A pdb=" N LEU D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.547A pdb=" N VAL D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.717A pdb=" N ALA D 191 " --> pdb=" O TYR D 188 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 192 " --> pdb=" O PHE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.583A pdb=" N LYS D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.776A pdb=" N VAL D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 349 through 362 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 50 through 54 removed outlier: 4.290A pdb=" N ALA E 54 " --> pdb=" O ASP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.577A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 88 removed outlier: 5.860A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 removed outlier: 4.025A pdb=" N ASP E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 256 through 261 Processing helix chain 'E' and resid 279 through 286 removed outlier: 4.409A pdb=" N ASN E 282 " --> pdb=" O SER E 279 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 284 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 285 " --> pdb=" O ASN E 282 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG E 286 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 313 Processing helix chain 'E' and resid 329 through 332 Processing helix chain 'E' and resid 349 through 361 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 74 through 89 removed outlier: 4.306A pdb=" N TRP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.811A pdb=" N LYS F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 233 through 249 removed outlier: 3.508A pdb=" N HIS F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.583A pdb=" N PHE F 284 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG F 286 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 315 removed outlier: 3.514A pdb=" N GLN F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 365 through 370 removed outlier: 3.658A pdb=" N GLN F 370 " --> pdb=" O TRP F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 49 through 56 removed outlier: 5.248A pdb=" N ALA G 54 " --> pdb=" O ASP G 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 56 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 76 through 89 removed outlier: 3.936A pdb=" N LYS G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 96 removed outlier: 3.547A pdb=" N ASP G 95 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 122 through 135 removed outlier: 3.510A pdb=" N GLN G 135 " --> pdb=" O ASN G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.528A pdb=" N LYS G 250 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.616A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 314 removed outlier: 3.528A pdb=" N GLN G 299 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 332 Processing helix chain 'G' and resid 349 through 363 Processing helix chain 'G' and resid 368 through 372 removed outlier: 3.782A pdb=" N LYS G 371 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.534A pdb=" N LEU H 56 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.665A pdb=" N GLY H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 250 Processing helix chain 'H' and resid 280 through 285 removed outlier: 3.652A pdb=" N VAL H 285 " --> pdb=" O ASN H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 315 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 363 Processing helix chain 'H' and resid 365 through 370 removed outlier: 3.643A pdb=" N GLN H 370 " --> pdb=" O TRP H 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 47 Processing helix chain 'I' and resid 49 through 55 Processing helix chain 'I' and resid 139 through 144 Processing helix chain 'I' and resid 223 through 231 Processing helix chain 'I' and resid 233 through 248 Processing helix chain 'I' and resid 281 through 286 removed outlier: 3.622A pdb=" N VAL I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 315 Processing helix chain 'I' and resid 328 through 332 Processing helix chain 'I' and resid 339 through 343 Processing helix chain 'I' and resid 349 through 362 removed outlier: 3.603A pdb=" N GLY I 362 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 110 Processing helix chain 'J' and resid 120 through 143 removed outlier: 3.541A pdb=" N ARG J 124 " --> pdb=" O ASN J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 163 removed outlier: 3.636A pdb=" N ASN J 163 " --> pdb=" O TRP J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 167 Processing helix chain 'J' and resid 189 through 192 Processing helix chain 'J' and resid 217 through 225 Processing helix chain 'J' and resid 255 through 263 removed outlier: 3.606A pdb=" N ALA J 261 " --> pdb=" O ALA J 257 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN J 262 " --> pdb=" O GLY J 258 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN J 263 " --> pdb=" O MET J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 292 Processing helix chain 'J' and resid 418 through 426 Processing helix chain 'J' and resid 427 through 438 removed outlier: 3.777A pdb=" N LYS J 438 " --> pdb=" O ALA J 434 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 465 removed outlier: 3.809A pdb=" N ALA J 454 " --> pdb=" O THR J 450 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE J 456 " --> pdb=" O GLN J 452 " (cutoff:3.500A) Proline residue: J 458 - end of helix removed outlier: 3.502A pdb=" N ASN J 462 " --> pdb=" O PRO J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 474 removed outlier: 3.933A pdb=" N GLU J 473 " --> pdb=" O GLY J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 483 Processing helix chain 'J' and resid 486 through 498 removed outlier: 3.669A pdb=" N THR J 491 " --> pdb=" O GLY J 487 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS J 492 " --> pdb=" O GLU J 488 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER J 496 " --> pdb=" O LYS J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 514 removed outlier: 3.819A pdb=" N ARG J 506 " --> pdb=" O THR J 502 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER J 514 " --> pdb=" O GLY J 510 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 Processing helix chain 'K' and resid 16 through 25 Processing helix chain 'K' and resid 34 through 52 Proline residue: K 47 - end of helix Processing helix chain 'K' and resid 57 through 71 Processing helix chain 'K' and resid 80 through 90 Processing helix chain 'K' and resid 96 through 107 removed outlier: 3.544A pdb=" N ARG K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 111 Processing helix chain 'K' and resid 113 through 115 No H-bonds generated for 'chain 'K' and resid 113 through 115' Processing helix chain 'K' and resid 116 through 130 removed outlier: 3.549A pdb=" N LEU K 120 " --> pdb=" O MET K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 149 through 165 removed outlier: 4.057A pdb=" N LYS K 153 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 17 removed outlier: 6.855A pdb=" N THR A 7 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 142 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 9 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 140 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG A 11 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 138 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 13 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER A 136 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 15 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 17 removed outlier: 6.855A pdb=" N THR A 7 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 142 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 9 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 140 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG A 11 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 138 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 13 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER A 136 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 15 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N THR A 124 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 85 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 126 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS A 83 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 128 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP A 81 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A 130 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP A 79 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU A 132 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 77 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP A 134 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET A 68 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG A 74 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N ILE A 207 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ARG A 241 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 243 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 74 removed outlier: 4.039A pdb=" N TYR B 3 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU B 8 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 186 through 207 removed outlier: 6.650A pdb=" N VAL B 235 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS B 189 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 233 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU B 191 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 231 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN B 193 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA B 229 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY B 195 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 227 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 197 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 225 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY B 199 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 223 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS B 201 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 221 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU B 203 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B 219 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS B 205 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP B 217 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.782A pdb=" N CYS D 27 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 35 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.782A pdb=" N CYS D 27 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 35 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 268 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.706A pdb=" N VAL D 101 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 326 through 327 removed outlier: 6.297A pdb=" N TRP D 326 " --> pdb=" O ILE D 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.792A pdb=" N VAL E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 35 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 177 " --> pdb=" O TYR E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.792A pdb=" N VAL E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 35 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 177 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY E 268 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL E 271 " --> pdb=" O PHE E 325 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE E 323 " --> pdb=" O PHE E 273 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY E 324 " --> pdb=" O ARG E 345 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE E 347 " --> pdb=" O GLY E 324 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TRP E 326 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.781A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.781A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE F 323 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLY F 324 " --> pdb=" O ARG F 345 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 347 " --> pdb=" O GLY F 324 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP F 326 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'F' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'G' and resid 26 through 29 removed outlier: 3.538A pdb=" N VAL G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 26 through 29 removed outlier: 3.538A pdb=" N VAL G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 323 " --> pdb=" O PHE G 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'H' and resid 26 through 29 removed outlier: 3.647A pdb=" N CYS H 27 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY H 324 " --> pdb=" O ARG H 345 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILE H 347 " --> pdb=" O GLY H 324 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP H 326 " --> pdb=" O ILE H 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 58 through 61 removed outlier: 3.529A pdb=" N THR H 61 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL H 101 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AC7, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.815A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 177 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE I 323 " --> pdb=" O PHE I 273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AC9, first strand: chain 'J' and resid 99 through 102 Processing sheet with id=AD1, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AD2, first strand: chain 'J' and resid 248 through 252 removed outlier: 4.477A pdb=" N LYS J 389 " --> pdb=" O HIS J 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP J 398 " --> pdb=" O SER J 402 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER J 402 " --> pdb=" O ASP J 398 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 305 through 306 Processing sheet with id=AD4, first strand: chain 'K' and resid 74 through 75 removed outlier: 5.622A pdb=" N GLU K 74 " --> pdb=" O LEU K 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 1030 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 9.04 Time building geometry restraints manager: 7.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8258 1.34 - 1.46: 4996 1.46 - 1.57: 14958 1.57 - 1.69: 120 1.69 - 1.81: 171 Bond restraints: 28503 Sorted by residual: bond pdb=" N PRO J 331 " pdb=" CD PRO J 331 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.62e+00 bond pdb=" C SER E 12 " pdb=" N PRO E 13 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.28e+00 bond pdb=" C SER F 12 " pdb=" N PRO F 13 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" O5' U C 20 " pdb=" C5' U C 20 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.67e+00 bond pdb=" O5' U C 32 " pdb=" C5' U C 32 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.65e+00 ... (remaining 28498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 38175 2.00 - 3.99: 614 3.99 - 5.99: 80 5.99 - 7.98: 18 7.98 - 9.98: 2 Bond angle restraints: 38889 Sorted by residual: angle pdb=" C THR D 123 " pdb=" N GLU D 124 " pdb=" CA GLU D 124 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C GLN F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta sigma weight residual 122.83 126.47 -3.64 1.08e+00 8.57e-01 1.14e+01 angle pdb=" C THR A 31 " pdb=" N ALA A 32 " pdb=" CA ALA A 32 " ideal model delta sigma weight residual 121.54 115.45 6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C ASP I 317 " pdb=" N GLU I 318 " pdb=" CA GLU I 318 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N GLY A 42 " pdb=" CA GLY A 42 " pdb=" C GLY A 42 " ideal model delta sigma weight residual 113.18 105.67 7.51 2.37e+00 1.78e-01 1.01e+01 ... (remaining 38884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 16131 34.77 - 69.54: 993 69.54 - 104.31: 80 104.31 - 139.08: 1 139.08 - 173.85: 3 Dihedral angle restraints: 17208 sinusoidal: 7483 harmonic: 9725 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual 200.00 34.90 165.10 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' U C 32 " pdb=" C1' U C 32 " pdb=" N1 U C 32 " pdb=" C2 U C 32 " ideal model delta sinusoidal sigma weight residual 200.00 47.39 152.61 1 1.50e+01 4.44e-03 8.05e+01 dihedral pdb=" O4' U C 2 " pdb=" C1' U C 2 " pdb=" N1 U C 2 " pdb=" C2 U C 2 " ideal model delta sinusoidal sigma weight residual -128.00 45.85 -173.85 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3009 0.041 - 0.082: 945 0.082 - 0.123: 281 0.123 - 0.164: 47 0.164 - 0.204: 1 Chirality restraints: 4283 Sorted by residual: chirality pdb=" C1' G C 14 " pdb=" O4' G C 14 " pdb=" C2' G C 14 " pdb=" N9 G C 14 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2' U C 20 " pdb=" C3' U C 20 " pdb=" O2' U C 20 " pdb=" C1' U C 20 " both_signs ideal model delta sigma weight residual False -2.75 -2.59 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CB VAL H 129 " pdb=" CA VAL H 129 " pdb=" CG1 VAL H 129 " pdb=" CG2 VAL H 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 4280 not shown) Planarity restraints: 4830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 144 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO A 145 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 398 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASP J 398 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP J 398 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP J 398 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 361 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE E 361 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE E 361 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY E 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 4827 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4697 2.77 - 3.30: 24552 3.30 - 3.83: 45788 3.83 - 4.37: 52539 4.37 - 4.90: 92745 Nonbonded interactions: 220321 Sorted by model distance: nonbonded pdb=" ND1 HIS B 135 " pdb=" OP1 U C 55 " model vdw 2.234 3.120 nonbonded pdb=" O ALA H 247 " pdb=" CG2 THR H 251 " model vdw 2.237 3.460 nonbonded pdb=" O LEU D 149 " pdb=" OG1 THR D 165 " model vdw 2.256 3.040 nonbonded pdb=" O LEU J 226 " pdb=" OG1 THR J 230 " model vdw 2.270 3.040 nonbonded pdb=" O CYS J 138 " pdb=" OG1 THR J 142 " model vdw 2.274 3.040 ... (remaining 220316 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 'D' and resid 1 through 370) selection = chain 'E' selection = (chain 'F' and resid 1 through 370) selection = (chain 'G' and resid 1 through 370) selection = (chain 'H' and resid 1 through 370) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.120 Check model and map are aligned: 0.220 Set scattering table: 0.240 Process input model: 68.560 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.003 0.043 28511 Z= 0.161 Angle : 0.627 9.981 38901 Z= 0.332 Chirality : 0.044 0.204 4283 Planarity : 0.005 0.060 4830 Dihedral : 20.077 173.850 10940 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.14 % Allowed : 35.80 % Favored : 64.06 % 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: -1.49 (0.14), residues: 3337 helix: -0.49 (0.15), residues: 1165 sheet: 0.19 (0.22), residues: 555 loop : -1.80 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 159 HIS 0.005 0.001 HIS F 6 PHE 0.016 0.001 PHE F 260 TYR 0.020 0.001 TYR E 360 ARG 0.008 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.18729 ( 1015) hydrogen bonds : angle 6.40923 ( 2890) metal coordination : bond 0.00472 ( 8) metal coordination : angle 2.96261 ( 12) covalent geometry : bond 0.00347 (28503) covalent geometry : angle 0.62488 (38889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 284 average time/residue: 0.3998 time to fit residues: 178.6058 Evaluate side-chains 279 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain G residue 233 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 172 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 306 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 225 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128438 restraints weight = 36410.729| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.38 r_work: 0.3332 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28511 Z= 0.153 Angle : 0.546 8.318 38901 Z= 0.285 Chirality : 0.041 0.196 4283 Planarity : 0.004 0.050 4830 Dihedral : 12.812 177.051 4563 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.65 % Allowed : 32.36 % Favored : 63.98 % 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: -0.92 (0.15), residues: 3337 helix: 0.28 (0.16), residues: 1161 sheet: 0.32 (0.22), residues: 537 loop : -1.61 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 156 HIS 0.004 0.001 HIS F 6 PHE 0.014 0.001 PHE G 219 TYR 0.013 0.001 TYR D 337 ARG 0.007 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1015) hydrogen bonds : angle 4.80393 ( 2890) metal coordination : bond 0.00488 ( 8) metal coordination : angle 2.86151 ( 12) covalent geometry : bond 0.00348 (28503) covalent geometry : angle 0.54375 (38889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 298 time to evaluate : 2.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 TYR cc_start: 0.6940 (m-80) cc_final: 0.6703 (m-80) REVERT: A 232 ASP cc_start: 0.7957 (p0) cc_final: 0.7734 (p0) REVERT: D 222 ASP cc_start: 0.8637 (t70) cc_final: 0.8415 (t0) REVERT: E 1 MET cc_start: 0.7665 (ttp) cc_final: 0.7431 (ttp) REVERT: F 148 MET cc_start: 0.5010 (tpt) cc_final: 0.4782 (tpt) REVERT: G 4 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8366 (mm-30) REVERT: G 148 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8238 (tmm) REVERT: G 233 ASP cc_start: 0.5936 (m-30) cc_final: 0.5733 (m-30) REVERT: G 337 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6751 (m-10) REVERT: G 352 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6476 (mp0) REVERT: H 4 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7907 (mm-30) REVERT: H 47 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8092 (ptt-90) REVERT: H 209 MET cc_start: 0.8824 (mtt) cc_final: 0.8612 (mtm) REVERT: I 298 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: J 230 THR cc_start: 0.8644 (m) cc_final: 0.8211 (p) REVERT: J 262 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6768 (mp10) REVERT: J 363 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7616 (ptt-90) REVERT: K 92 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7270 (mt) outliers start: 103 outliers final: 50 residues processed: 378 average time/residue: 0.3973 time to fit residues: 236.7567 Evaluate side-chains 334 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 101 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 324 optimal weight: 0.4980 chunk 183 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 225 GLN E 229 ASN F 82 GLN F 135 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN I 172 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.169498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124262 restraints weight = 36869.163| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.54 r_work: 0.3275 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 28511 Z= 0.259 Angle : 0.628 8.949 38901 Z= 0.327 Chirality : 0.045 0.234 4283 Planarity : 0.004 0.055 4830 Dihedral : 12.774 169.279 4559 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 4.96 % Allowed : 31.97 % Favored : 63.06 % 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: -1.02 (0.15), residues: 3337 helix: 0.25 (0.16), residues: 1162 sheet: 0.16 (0.22), residues: 538 loop : -1.68 (0.15), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 156 HIS 0.006 0.001 HIS F 6 PHE 0.020 0.002 PHE G 219 TYR 0.021 0.002 TYR F 316 ARG 0.005 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 1015) hydrogen bonds : angle 4.82190 ( 2890) metal coordination : bond 0.00663 ( 8) metal coordination : angle 3.62944 ( 12) covalent geometry : bond 0.00605 (28503) covalent geometry : angle 0.62502 (38889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 292 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 240 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7693 (t70) REVERT: D 222 ASP cc_start: 0.8735 (t70) cc_final: 0.8511 (t0) REVERT: E 1 MET cc_start: 0.7642 (ttp) cc_final: 0.7378 (ttp) REVERT: E 19 ASP cc_start: 0.8357 (t70) cc_final: 0.8101 (t70) REVERT: E 76 GLU cc_start: 0.3457 (OUTLIER) cc_final: 0.2523 (pm20) REVERT: F 82 GLN cc_start: 0.4973 (OUTLIER) cc_final: 0.4192 (mp-120) REVERT: F 148 MET cc_start: 0.5464 (tpt) cc_final: 0.5240 (tpt) REVERT: F 159 LYS cc_start: 0.5252 (OUTLIER) cc_final: 0.4981 (tppt) REVERT: F 337 TYR cc_start: 0.7866 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: G 148 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8255 (tmm) REVERT: G 337 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6949 (m-10) REVERT: G 352 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: H 4 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7768 (mt-10) REVERT: H 156 LYS cc_start: 0.3163 (OUTLIER) cc_final: 0.2566 (mtmt) REVERT: H 295 ASP cc_start: 0.8592 (m-30) cc_final: 0.8243 (m-30) REVERT: J 262 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6712 (mp10) REVERT: J 319 GLU cc_start: 0.6035 (tm-30) cc_final: 0.5771 (tm-30) REVERT: J 445 LYS cc_start: 0.7153 (tttt) cc_final: 0.6494 (tttt) REVERT: K 92 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7334 (mt) REVERT: K 96 LYS cc_start: 0.7587 (mmtp) cc_final: 0.7330 (mmmm) outliers start: 140 outliers final: 77 residues processed: 405 average time/residue: 0.4100 time to fit residues: 257.6809 Evaluate side-chains 366 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 277 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 337 TYR Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 113 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 321 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 chunk 249 optimal weight: 0.0070 chunk 68 optimal weight: 8.9990 chunk 188 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 318 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 295 optimal weight: 9.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN E 17 ASN E 252 ASN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.170085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125154 restraints weight = 37117.669| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.67 r_work: 0.3276 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28511 Z= 0.226 Angle : 0.594 8.669 38901 Z= 0.309 Chirality : 0.043 0.231 4283 Planarity : 0.004 0.046 4830 Dihedral : 12.725 167.481 4559 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.79 % Allowed : 32.15 % Favored : 63.06 % 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: -0.98 (0.15), residues: 3337 helix: 0.37 (0.16), residues: 1159 sheet: 0.12 (0.22), residues: 543 loop : -1.70 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 156 HIS 0.008 0.001 HIS I 204 PHE 0.016 0.002 PHE G 219 TYR 0.019 0.002 TYR F 316 ARG 0.007 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 1015) hydrogen bonds : angle 4.72230 ( 2890) metal coordination : bond 0.00595 ( 8) metal coordination : angle 3.25296 ( 12) covalent geometry : bond 0.00530 (28503) covalent geometry : angle 0.59093 (38889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 284 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 240 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7693 (t70) REVERT: D 165 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.7938 (t) REVERT: D 222 ASP cc_start: 0.8701 (t70) cc_final: 0.8485 (t0) REVERT: D 269 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8369 (mm) REVERT: E 1 MET cc_start: 0.7507 (ttp) cc_final: 0.7212 (ttp) REVERT: E 76 GLU cc_start: 0.3322 (OUTLIER) cc_final: 0.2425 (pm20) REVERT: F 131 ASN cc_start: 0.7211 (OUTLIER) cc_final: 0.6977 (t0) REVERT: F 148 MET cc_start: 0.5666 (tpt) cc_final: 0.5258 (tpt) REVERT: G 76 GLU cc_start: 0.5440 (OUTLIER) cc_final: 0.5012 (pm20) REVERT: G 148 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8240 (tmm) REVERT: G 337 TYR cc_start: 0.7323 (OUTLIER) cc_final: 0.6999 (m-10) REVERT: H 2 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8374 (mp) REVERT: H 4 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: H 102 PHE cc_start: 0.8201 (t80) cc_final: 0.7965 (t80) REVERT: H 295 ASP cc_start: 0.8559 (m-30) cc_final: 0.8205 (m-30) REVERT: J 230 THR cc_start: 0.8781 (m) cc_final: 0.8237 (p) REVERT: J 259 MET cc_start: 0.6670 (tpp) cc_final: 0.6070 (ttp) REVERT: J 262 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.6690 (mp10) REVERT: J 319 GLU cc_start: 0.6044 (tm-30) cc_final: 0.5806 (tm-30) REVERT: J 445 LYS cc_start: 0.7217 (tttt) cc_final: 0.6453 (tttt) REVERT: K 92 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7389 (mt) REVERT: K 96 LYS cc_start: 0.7514 (mmtp) cc_final: 0.7262 (mmmm) outliers start: 135 outliers final: 85 residues processed: 391 average time/residue: 0.3967 time to fit residues: 244.5891 Evaluate side-chains 373 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 276 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain H residue 2 LEU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 174 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 251 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 219 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 ASN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.171073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125303 restraints weight = 36667.675| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.62 r_work: 0.3295 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28511 Z= 0.184 Angle : 0.562 9.370 38901 Z= 0.291 Chirality : 0.042 0.219 4283 Planarity : 0.004 0.045 4830 Dihedral : 12.653 167.341 4559 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 5.64 % Allowed : 31.41 % Favored : 62.96 % 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: -0.86 (0.15), residues: 3337 helix: 0.55 (0.16), residues: 1156 sheet: 0.12 (0.22), residues: 545 loop : -1.67 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 156 HIS 0.005 0.001 HIS F 6 PHE 0.014 0.001 PHE G 219 TYR 0.015 0.001 TYR F 316 ARG 0.006 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 1015) hydrogen bonds : angle 4.55235 ( 2890) metal coordination : bond 0.00669 ( 8) metal coordination : angle 4.02910 ( 12) covalent geometry : bond 0.00429 (28503) covalent geometry : angle 0.55748 (38889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 291 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 379 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7277 (ttm-80) REVERT: B 240 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7695 (t70) REVERT: D 56 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6828 (tp) REVERT: D 103 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7280 (tpt) REVERT: D 165 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.7870 (t) REVERT: D 222 ASP cc_start: 0.8676 (t70) cc_final: 0.8434 (t0) REVERT: E 1 MET cc_start: 0.7497 (ttp) cc_final: 0.7221 (ttp) REVERT: E 76 GLU cc_start: 0.3280 (OUTLIER) cc_final: 0.2409 (pm20) REVERT: F 82 GLN cc_start: 0.4613 (OUTLIER) cc_final: 0.3803 (mp-120) REVERT: F 131 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.7067 (t0) REVERT: F 148 MET cc_start: 0.5826 (tpt) cc_final: 0.5414 (tpt) REVERT: F 159 LYS cc_start: 0.5225 (OUTLIER) cc_final: 0.4951 (tppt) REVERT: F 171 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9096 (tp) REVERT: G 148 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8184 (tmm) REVERT: G 156 LYS cc_start: 0.5504 (OUTLIER) cc_final: 0.4755 (mtpp) REVERT: G 337 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6982 (m-10) REVERT: H 4 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7824 (mm-30) REVERT: H 47 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8090 (ptt-90) REVERT: H 102 PHE cc_start: 0.8083 (t80) cc_final: 0.7846 (t80) REVERT: H 156 LYS cc_start: 0.3478 (OUTLIER) cc_final: 0.2994 (mtmt) REVERT: H 295 ASP cc_start: 0.8465 (m-30) cc_final: 0.8113 (m-30) REVERT: J 230 THR cc_start: 0.8737 (m) cc_final: 0.8204 (p) REVERT: J 259 MET cc_start: 0.6615 (tpp) cc_final: 0.6194 (ttp) REVERT: J 262 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.7076 (mp10) REVERT: J 319 GLU cc_start: 0.6018 (tm-30) cc_final: 0.5745 (tm-30) REVERT: J 445 LYS cc_start: 0.7247 (tttt) cc_final: 0.6677 (tttt) REVERT: K 92 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7427 (mt) REVERT: K 96 LYS cc_start: 0.7442 (mmtp) cc_final: 0.7215 (mmmm) REVERT: K 161 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7758 (mp) outliers start: 159 outliers final: 106 residues processed: 425 average time/residue: 0.3822 time to fit residues: 255.0104 Evaluate side-chains 402 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 277 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 379 ARG Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 156 LYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 98 optimal weight: 7.9990 chunk 212 optimal weight: 0.0570 chunk 58 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 286 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.172489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127042 restraints weight = 36762.319| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.61 r_work: 0.3314 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28511 Z= 0.135 Angle : 0.533 8.913 38901 Z= 0.275 Chirality : 0.041 0.201 4283 Planarity : 0.004 0.044 4830 Dihedral : 12.583 166.968 4559 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 4.93 % Allowed : 32.12 % Favored : 62.96 % 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: -0.69 (0.15), residues: 3337 helix: 0.72 (0.16), residues: 1154 sheet: 0.23 (0.22), residues: 545 loop : -1.61 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 159 HIS 0.004 0.001 HIS F 6 PHE 0.012 0.001 PHE F 260 TYR 0.012 0.001 TYR F 316 ARG 0.008 0.000 ARG J 363 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 1015) hydrogen bonds : angle 4.41329 ( 2890) metal coordination : bond 0.00493 ( 8) metal coordination : angle 3.67255 ( 12) covalent geometry : bond 0.00309 (28503) covalent geometry : angle 0.52915 (38889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 295 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6612 (ptt180) REVERT: A 232 ASP cc_start: 0.8227 (p0) cc_final: 0.7875 (p0) REVERT: B 240 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7695 (t70) REVERT: D 165 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7793 (t) REVERT: D 222 ASP cc_start: 0.8666 (t70) cc_final: 0.8349 (t0) REVERT: E 1 MET cc_start: 0.7393 (ttp) cc_final: 0.7108 (ttp) REVERT: E 76 GLU cc_start: 0.3152 (OUTLIER) cc_final: 0.2339 (pm20) REVERT: F 148 MET cc_start: 0.5867 (tpt) cc_final: 0.5181 (tpt) REVERT: F 159 LYS cc_start: 0.5259 (OUTLIER) cc_final: 0.5015 (tppt) REVERT: G 337 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: G 352 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6294 (mp0) REVERT: H 4 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8008 (mm-30) REVERT: H 47 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7997 (ptt-90) REVERT: H 156 LYS cc_start: 0.3321 (OUTLIER) cc_final: 0.2806 (mtmt) REVERT: H 209 MET cc_start: 0.8822 (mtt) cc_final: 0.8591 (mtm) REVERT: H 295 ASP cc_start: 0.8302 (m-30) cc_final: 0.8038 (m-30) REVERT: J 230 THR cc_start: 0.8651 (m) cc_final: 0.8120 (p) REVERT: J 259 MET cc_start: 0.6401 (tpp) cc_final: 0.6017 (ttp) REVERT: J 262 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6968 (mp10) REVERT: J 319 GLU cc_start: 0.5878 (tm-30) cc_final: 0.5572 (tm-30) REVERT: J 418 ASN cc_start: 0.7162 (p0) cc_final: 0.6612 (p0) REVERT: J 445 LYS cc_start: 0.7246 (tttt) cc_final: 0.6726 (tttt) REVERT: K 92 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7353 (mt) REVERT: K 161 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7671 (mp) outliers start: 139 outliers final: 97 residues processed: 411 average time/residue: 0.4085 time to fit residues: 261.5899 Evaluate side-chains 391 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 281 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain J residue 520 ILE Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 330 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.170488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125176 restraints weight = 36670.377| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.41 r_work: 0.3294 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 28511 Z= 0.216 Angle : 0.588 9.044 38901 Z= 0.304 Chirality : 0.043 0.219 4283 Planarity : 0.004 0.043 4830 Dihedral : 12.626 167.826 4559 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 5.67 % Allowed : 31.05 % Favored : 63.28 % 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: -0.82 (0.15), residues: 3337 helix: 0.58 (0.16), residues: 1157 sheet: 0.14 (0.22), residues: 545 loop : -1.65 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 159 HIS 0.006 0.001 HIS F 6 PHE 0.018 0.002 PHE D 102 TYR 0.017 0.002 TYR F 316 ARG 0.006 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 1015) hydrogen bonds : angle 4.54876 ( 2890) metal coordination : bond 0.00614 ( 8) metal coordination : angle 3.85398 ( 12) covalent geometry : bond 0.00509 (28503) covalent geometry : angle 0.58443 (38889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 285 time to evaluate : 3.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 56 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6782 (tp) REVERT: D 78 TRP cc_start: 0.7000 (OUTLIER) cc_final: 0.5620 (t60) REVERT: D 165 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.7884 (t) REVERT: D 222 ASP cc_start: 0.8735 (t70) cc_final: 0.8443 (t0) REVERT: E 1 MET cc_start: 0.7521 (ttp) cc_final: 0.7235 (ttp) REVERT: E 76 GLU cc_start: 0.3284 (OUTLIER) cc_final: 0.2452 (pm20) REVERT: E 254 SER cc_start: 0.8617 (p) cc_final: 0.8346 (p) REVERT: F 82 GLN cc_start: 0.4812 (OUTLIER) cc_final: 0.3916 (mp-120) REVERT: F 148 MET cc_start: 0.6133 (tpt) cc_final: 0.5363 (tpt) REVERT: F 159 LYS cc_start: 0.5222 (OUTLIER) cc_final: 0.4931 (tppt) REVERT: F 171 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9106 (tp) REVERT: G 76 GLU cc_start: 0.5433 (OUTLIER) cc_final: 0.5027 (pm20) REVERT: G 337 TYR cc_start: 0.7319 (OUTLIER) cc_final: 0.6933 (m-10) REVERT: G 352 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: H 4 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: H 47 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8082 (ptt-90) REVERT: H 102 PHE cc_start: 0.8193 (t80) cc_final: 0.7902 (t80) REVERT: H 156 LYS cc_start: 0.3523 (OUTLIER) cc_final: 0.3085 (mtmt) REVERT: H 295 ASP cc_start: 0.8455 (m-30) cc_final: 0.8113 (m-30) REVERT: J 230 THR cc_start: 0.8755 (m) cc_final: 0.8219 (p) REVERT: J 259 MET cc_start: 0.6603 (tpp) cc_final: 0.6183 (ttp) REVERT: J 262 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7051 (mp10) REVERT: J 319 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5711 (tm-30) REVERT: J 358 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9059 (mp) REVERT: J 418 ASN cc_start: 0.7198 (p0) cc_final: 0.6800 (p0) REVERT: J 445 LYS cc_start: 0.7288 (tttt) cc_final: 0.6801 (tttt) REVERT: K 92 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7378 (mt) REVERT: K 96 LYS cc_start: 0.7468 (mmtp) cc_final: 0.7223 (mmmm) REVERT: K 124 MET cc_start: 0.8964 (OUTLIER) cc_final: 0.7749 (mtt) outliers start: 160 outliers final: 124 residues processed: 421 average time/residue: 0.4051 time to fit residues: 266.6437 Evaluate side-chains 419 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 278 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 256 LYS Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 289 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 358 LEU Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 335 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 173 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 202 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN E 127 GLN F 82 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 GLN ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.172977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.127189 restraints weight = 36558.408| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.63 r_work: 0.3322 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28511 Z= 0.124 Angle : 0.531 8.686 38901 Z= 0.275 Chirality : 0.041 0.196 4283 Planarity : 0.004 0.042 4830 Dihedral : 12.537 167.062 4559 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.64 % Allowed : 32.26 % Favored : 63.10 % 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: -0.61 (0.15), residues: 3337 helix: 0.82 (0.16), residues: 1158 sheet: 0.29 (0.22), residues: 545 loop : -1.60 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 159 HIS 0.004 0.001 HIS G 204 PHE 0.013 0.001 PHE D 102 TYR 0.011 0.001 TYR A 283 ARG 0.008 0.000 ARG J 363 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 1015) hydrogen bonds : angle 4.34132 ( 2890) metal coordination : bond 0.00416 ( 8) metal coordination : angle 3.22985 ( 12) covalent geometry : bond 0.00281 (28503) covalent geometry : angle 0.52760 (38889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 290 time to evaluate : 2.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6709 (ptt180) REVERT: A 232 ASP cc_start: 0.8250 (p0) cc_final: 0.7945 (p0) REVERT: B 203 GLU cc_start: 0.7536 (tt0) cc_final: 0.7265 (mt-10) REVERT: D 56 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6721 (tp) REVERT: D 67 LEU cc_start: 0.7941 (tp) cc_final: 0.6953 (mm) REVERT: D 165 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.7796 (t) REVERT: D 222 ASP cc_start: 0.8635 (t70) cc_final: 0.8364 (t0) REVERT: D 312 ARG cc_start: 0.6619 (mmm160) cc_final: 0.6345 (mmm160) REVERT: E 1 MET cc_start: 0.7508 (ttp) cc_final: 0.7229 (ttp) REVERT: E 76 GLU cc_start: 0.3132 (OUTLIER) cc_final: 0.2321 (pm20) REVERT: E 127 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: E 161 LYS cc_start: 0.6855 (mmmt) cc_final: 0.5888 (ptmm) REVERT: F 82 GLN cc_start: 0.4682 (OUTLIER) cc_final: 0.3691 (mp-120) REVERT: F 148 MET cc_start: 0.6081 (tpt) cc_final: 0.5595 (tpt) REVERT: F 171 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9090 (tp) REVERT: G 318 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7351 (tm-30) REVERT: G 337 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: H 4 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7967 (mm-30) REVERT: H 47 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8075 (ptt-90) REVERT: H 156 LYS cc_start: 0.3407 (OUTLIER) cc_final: 0.2982 (mtmt) REVERT: H 209 MET cc_start: 0.8828 (mtt) cc_final: 0.8620 (mtm) REVERT: H 295 ASP cc_start: 0.8353 (m-30) cc_final: 0.8068 (m-30) REVERT: J 230 THR cc_start: 0.8676 (m) cc_final: 0.8162 (p) REVERT: J 259 MET cc_start: 0.6504 (tpp) cc_final: 0.6086 (ttp) REVERT: J 262 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: J 319 GLU cc_start: 0.5979 (tm-30) cc_final: 0.5665 (tm-30) REVERT: J 328 GLU cc_start: 0.6351 (pp20) cc_final: 0.6031 (pp20) REVERT: J 418 ASN cc_start: 0.7185 (p0) cc_final: 0.6783 (p0) REVERT: J 445 LYS cc_start: 0.7337 (tttt) cc_final: 0.6891 (tttt) REVERT: K 92 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7347 (mt) REVERT: K 124 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7654 (mtt) REVERT: K 161 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7801 (mp) outliers start: 131 outliers final: 101 residues processed: 399 average time/residue: 0.4430 time to fit residues: 277.7132 Evaluate side-chains 397 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 281 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain J residue 520 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 83 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 253 optimal weight: 0.9990 chunk 313 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 216 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 320 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 274 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 82 GLN I 172 GLN ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.128015 restraints weight = 36627.498| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.62 r_work: 0.3336 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28511 Z= 0.110 Angle : 0.518 9.315 38901 Z= 0.267 Chirality : 0.040 0.183 4283 Planarity : 0.004 0.042 4830 Dihedral : 12.475 166.458 4559 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.32 % Allowed : 32.54 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.15), residues: 3337 helix: 0.89 (0.16), residues: 1167 sheet: 0.41 (0.22), residues: 537 loop : -1.55 (0.16), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 159 HIS 0.004 0.001 HIS G 204 PHE 0.012 0.001 PHE D 102 TYR 0.015 0.001 TYR E 316 ARG 0.008 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 1015) hydrogen bonds : angle 4.24778 ( 2890) metal coordination : bond 0.00367 ( 8) metal coordination : angle 3.10470 ( 12) covalent geometry : bond 0.00246 (28503) covalent geometry : angle 0.51546 (38889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 298 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6716 (ptt180) REVERT: A 232 ASP cc_start: 0.8150 (p0) cc_final: 0.7829 (p0) REVERT: B 203 GLU cc_start: 0.7528 (tt0) cc_final: 0.7260 (mt-10) REVERT: D 56 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6621 (tp) REVERT: D 67 LEU cc_start: 0.7958 (tp) cc_final: 0.6968 (mm) REVERT: D 165 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7822 (t) REVERT: D 222 ASP cc_start: 0.8637 (t70) cc_final: 0.8351 (t0) REVERT: D 312 ARG cc_start: 0.6632 (mmm160) cc_final: 0.6381 (mmm160) REVERT: E 1 MET cc_start: 0.7526 (ttp) cc_final: 0.7234 (ttp) REVERT: E 76 GLU cc_start: 0.3157 (OUTLIER) cc_final: 0.2323 (pm20) REVERT: F 82 GLN cc_start: 0.4491 (OUTLIER) cc_final: 0.3590 (mp-120) REVERT: F 148 MET cc_start: 0.6122 (tpt) cc_final: 0.5886 (tpt) REVERT: F 171 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9086 (tp) REVERT: G 337 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: H 4 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7965 (mm-30) REVERT: H 47 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8034 (ptt-90) REVERT: H 156 LYS cc_start: 0.3401 (OUTLIER) cc_final: 0.2951 (mtmt) REVERT: J 230 THR cc_start: 0.8660 (m) cc_final: 0.8167 (p) REVERT: J 259 MET cc_start: 0.6465 (tpp) cc_final: 0.6133 (ttp) REVERT: J 262 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: J 319 GLU cc_start: 0.5981 (tm-30) cc_final: 0.5652 (tm-30) REVERT: J 328 GLU cc_start: 0.6337 (pp20) cc_final: 0.6027 (pp20) REVERT: J 418 ASN cc_start: 0.7085 (p0) cc_final: 0.6692 (p0) REVERT: J 445 LYS cc_start: 0.7363 (tttt) cc_final: 0.6889 (tttt) REVERT: K 92 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7310 (mt) REVERT: K 124 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.7570 (mtt) REVERT: K 161 ILE cc_start: 0.8029 (OUTLIER) cc_final: 0.7794 (mp) outliers start: 122 outliers final: 99 residues processed: 404 average time/residue: 0.4033 time to fit residues: 253.1037 Evaluate side-chains 400 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 287 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain J residue 520 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 183 optimal weight: 10.0000 chunk 299 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 2 optimal weight: 0.0000 chunk 144 optimal weight: 5.9990 chunk 319 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 135 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.172963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127772 restraints weight = 36539.797| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.42 r_work: 0.3332 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28511 Z= 0.143 Angle : 0.537 9.445 38901 Z= 0.277 Chirality : 0.041 0.189 4283 Planarity : 0.004 0.040 4830 Dihedral : 12.463 166.568 4559 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.54 % Allowed : 32.33 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.15), residues: 3337 helix: 0.88 (0.16), residues: 1167 sheet: 0.37 (0.22), residues: 545 loop : -1.54 (0.16), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 159 HIS 0.004 0.001 HIS G 204 PHE 0.013 0.001 PHE D 102 TYR 0.014 0.001 TYR B 29 ARG 0.008 0.000 ARG J 363 Details of bonding type rmsd hydrogen bonds : bond 0.03622 ( 1015) hydrogen bonds : angle 4.28718 ( 2890) metal coordination : bond 0.00433 ( 8) metal coordination : angle 3.18352 ( 12) covalent geometry : bond 0.00331 (28503) covalent geometry : angle 0.53442 (38889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 290 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6584 (ptt180) REVERT: A 144 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6381 (tm-30) REVERT: A 232 ASP cc_start: 0.8155 (p0) cc_final: 0.7829 (p0) REVERT: D 56 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6630 (tp) REVERT: D 67 LEU cc_start: 0.7977 (tp) cc_final: 0.6986 (mm) REVERT: D 78 TRP cc_start: 0.7013 (OUTLIER) cc_final: 0.5640 (t60) REVERT: D 165 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7812 (t) REVERT: D 222 ASP cc_start: 0.8659 (t70) cc_final: 0.8354 (t0) REVERT: D 312 ARG cc_start: 0.6661 (mmm160) cc_final: 0.6415 (mmm160) REVERT: E 1 MET cc_start: 0.7515 (ttp) cc_final: 0.7232 (ttp) REVERT: E 76 GLU cc_start: 0.3194 (OUTLIER) cc_final: 0.2344 (pm20) REVERT: E 105 LYS cc_start: 0.6412 (OUTLIER) cc_final: 0.5758 (mtmt) REVERT: F 148 MET cc_start: 0.6206 (tpt) cc_final: 0.5909 (tpt) REVERT: F 171 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9102 (tp) REVERT: G 337 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6877 (m-10) REVERT: G 352 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6380 (mp0) REVERT: H 4 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: H 47 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8021 (ptt-90) REVERT: H 156 LYS cc_start: 0.3443 (OUTLIER) cc_final: 0.2987 (mtmt) REVERT: H 295 ASP cc_start: 0.8290 (m-30) cc_final: 0.7988 (m-30) REVERT: J 230 THR cc_start: 0.8666 (m) cc_final: 0.8165 (p) REVERT: J 259 MET cc_start: 0.6483 (tpp) cc_final: 0.6148 (ttp) REVERT: J 262 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7019 (mp10) REVERT: J 319 GLU cc_start: 0.5987 (tm-30) cc_final: 0.5660 (tm-30) REVERT: J 328 GLU cc_start: 0.6314 (pp20) cc_final: 0.6006 (pp20) REVERT: J 418 ASN cc_start: 0.7028 (p0) cc_final: 0.6676 (p0) REVERT: J 445 LYS cc_start: 0.7389 (tttt) cc_final: 0.6922 (tttt) REVERT: K 92 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7303 (mt) REVERT: K 124 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.7568 (mtt) REVERT: K 161 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7757 (mp) outliers start: 128 outliers final: 107 residues processed: 402 average time/residue: 0.4124 time to fit residues: 259.0974 Evaluate side-chains 410 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 286 time to evaluate : 3.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 289 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain J residue 520 ILE Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 287 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 314 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 272 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 0.0670 chunk 81 optimal weight: 6.9990 overall best weight: 2.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.171321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119730 restraints weight = 36459.552| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.56 r_work: 0.3315 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 28511 Z= 0.192 Angle : 0.574 9.322 38901 Z= 0.297 Chirality : 0.042 0.208 4283 Planarity : 0.004 0.039 4830 Dihedral : 12.527 167.702 4559 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 4.71 % Allowed : 32.40 % Favored : 62.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.15), residues: 3337 helix: 0.79 (0.16), residues: 1156 sheet: 0.28 (0.22), residues: 545 loop : -1.56 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP J 159 HIS 0.006 0.001 HIS F 6 PHE 0.019 0.001 PHE D 102 TYR 0.015 0.001 TYR E 316 ARG 0.007 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1015) hydrogen bonds : angle 4.44235 ( 2890) metal coordination : bond 0.00528 ( 8) metal coordination : angle 3.54583 ( 12) covalent geometry : bond 0.00450 (28503) covalent geometry : angle 0.57092 (38889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17327.39 seconds wall clock time: 299 minutes 36.64 seconds (17976.64 seconds total)