Starting phenix.real_space_refine on Mon Aug 25 10:53:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yb6_39110/08_2025/8yb6_39110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yb6_39110/08_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_39110/08_2025/8yb6_39110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yb6_39110/08_2025/8yb6_39110.map" model { file = "/net/cci-nas-00/data/ceres_data/8yb6_39110/08_2025/8yb6_39110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yb6_39110/08_2025/8yb6_39110.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.080 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 6.53, per 1000 atoms: 0.24 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: 2.24 Conformation dependent library (CDL) restraints added in 934.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.72 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: 4.85 Time building geometry restraints manager: 2.91 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: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 28.730 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.580 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG H 60 TYR 0.020 0.001 TYR E 360 PHE 0.016 0.001 PHE F 260 TRP 0.025 0.001 TRP J 159 HIS 0.005 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00347 (28503) covalent geometry : angle 0.62488 (38889) hydrogen bonds : bond 0.18729 ( 1015) hydrogen bonds : angle 6.40923 ( 2890) metal coordination : bond 0.00472 ( 8) metal coordination : angle 2.96261 ( 12) *********************** 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 : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 284 average time/residue: 0.1747 time to fit residues: 78.9296 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 : 0.906 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0050 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.0060 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.7414 ------------------------------------------------------------------------------- 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 17 ASN E 225 GLN E 229 ASN G 225 GLN H 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.174294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128689 restraints weight = 36688.196| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.61 r_work: 0.3340 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28511 Z= 0.138 Angle : 0.537 8.082 38901 Z= 0.280 Chirality : 0.041 0.188 4283 Planarity : 0.004 0.050 4830 Dihedral : 12.794 177.271 4563 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.58 % Allowed : 32.26 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.15), residues: 3337 helix: 0.32 (0.16), residues: 1162 sheet: 0.34 (0.22), residues: 537 loop : -1.59 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 60 TYR 0.014 0.001 TYR D 337 PHE 0.014 0.001 PHE G 219 TRP 0.015 0.001 TRP K 156 HIS 0.003 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00310 (28503) covalent geometry : angle 0.53444 (38889) hydrogen bonds : bond 0.04332 ( 1015) hydrogen bonds : angle 4.73535 ( 2890) metal coordination : bond 0.00440 ( 8) metal coordination : angle 2.81363 ( 12) *********************** 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 400 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 299 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 TYR cc_start: 0.6877 (m-80) cc_final: 0.6630 (m-80) REVERT: A 232 ASP cc_start: 0.7906 (p0) cc_final: 0.7702 (p0) REVERT: D 222 ASP cc_start: 0.8601 (t70) cc_final: 0.8347 (t0) REVERT: F 148 MET cc_start: 0.4963 (tpt) cc_final: 0.4742 (tpt) REVERT: G 4 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8295 (mm-30) REVERT: G 76 GLU cc_start: 0.5260 (OUTLIER) cc_final: 0.4906 (pm20) REVERT: G 148 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8195 (tmm) REVERT: G 337 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6724 (m-10) REVERT: G 352 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: H 4 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7897 (mm-30) REVERT: H 47 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8069 (ptt-90) REVERT: H 209 MET cc_start: 0.8809 (mtt) cc_final: 0.8587 (mtm) REVERT: J 230 THR cc_start: 0.8619 (m) cc_final: 0.8189 (p) REVERT: J 262 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: J 363 ARG cc_start: 0.7823 (ptt-90) cc_final: 0.7587 (ptt-90) REVERT: K 92 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7271 (mt) outliers start: 101 outliers final: 46 residues processed: 378 average time/residue: 0.1650 time to fit residues: 99.1895 Evaluate side-chains 331 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 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 76 GLU 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 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 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 205 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 333 optimal weight: 7.9990 chunk 282 optimal weight: 0.7980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN E 86 ASN F 135 GLN I 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.128203 restraints weight = 36748.600| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.50 r_work: 0.3333 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0935 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= 0.142 Angle : 0.524 8.097 38901 Z= 0.272 Chirality : 0.041 0.191 4283 Planarity : 0.004 0.058 4830 Dihedral : 12.665 173.359 4559 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.97 % Allowed : 32.08 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.15), residues: 3337 helix: 0.59 (0.16), residues: 1164 sheet: 0.36 (0.22), residues: 545 loop : -1.58 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 326 TYR 0.011 0.001 TYR D 337 PHE 0.013 0.001 PHE G 219 TRP 0.015 0.001 TRP K 156 HIS 0.004 0.001 HIS F 6 Details of bonding type rmsd covalent geometry : bond 0.00326 (28503) covalent geometry : angle 0.52188 (38889) hydrogen bonds : bond 0.04069 ( 1015) hydrogen bonds : angle 4.47969 ( 2890) metal coordination : bond 0.00410 ( 8) metal coordination : angle 2.73507 ( 12) *********************** 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 406 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 294 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6741 (ptt180) REVERT: A 232 ASP cc_start: 0.7871 (p0) cc_final: 0.7665 (p0) REVERT: B 240 ASP cc_start: 0.7903 (OUTLIER) cc_final: 0.7701 (t70) REVERT: D 165 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.7842 (t) REVERT: D 222 ASP cc_start: 0.8648 (t70) cc_final: 0.8339 (t0) REVERT: E 76 GLU cc_start: 0.3339 (OUTLIER) cc_final: 0.2452 (pm20) REVERT: G 4 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8383 (mm-30) REVERT: G 76 GLU cc_start: 0.5279 (OUTLIER) cc_final: 0.4928 (pm20) REVERT: G 148 MET cc_start: 0.8465 (ttt) cc_final: 0.8225 (tmm) REVERT: G 337 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6826 (m-10) REVERT: G 352 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: H 4 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: H 47 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.8044 (ptt-90) REVERT: H 209 MET cc_start: 0.8786 (mtt) cc_final: 0.8575 (mtm) REVERT: H 295 ASP cc_start: 0.8303 (m-30) cc_final: 0.8065 (m-30) REVERT: I 298 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: J 230 THR cc_start: 0.8635 (m) cc_final: 0.8163 (p) REVERT: J 262 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: J 298 LYS cc_start: 0.6530 (mptt) cc_final: 0.6316 (mptt) REVERT: J 441 ARG cc_start: 0.8096 (ptp-170) cc_final: 0.7874 (mtm-85) REVERT: J 445 LYS cc_start: 0.7152 (tttt) cc_final: 0.6539 (tttt) REVERT: K 92 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7282 (mt) outliers start: 112 outliers final: 57 residues processed: 384 average time/residue: 0.1746 time to fit residues: 105.1785 Evaluate side-chains 348 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 278 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 211 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 77 ASP 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 240 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE 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 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 323 ILE Chi-restraints excluded: chain F residue 35 SER 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 4 GLU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 76 GLU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 160 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 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 323 ILE Chi-restraints excluded: chain H residue 344 SER 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 294 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 238 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 285 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 193 optimal weight: 0.0980 chunk 275 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 70 GLN I 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.173812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128518 restraints weight = 36415.783| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.45 r_work: 0.3340 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1061 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= 0.133 Angle : 0.515 8.600 38901 Z= 0.267 Chirality : 0.041 0.186 4283 Planarity : 0.004 0.049 4830 Dihedral : 12.577 171.667 4559 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 4.18 % Allowed : 32.08 % Favored : 63.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.15), residues: 3337 helix: 0.75 (0.16), residues: 1168 sheet: 0.40 (0.22), residues: 545 loop : -1.56 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 62 TYR 0.012 0.001 TYR E 316 PHE 0.012 0.001 PHE F 260 TRP 0.015 0.001 TRP K 156 HIS 0.007 0.001 HIS I 204 Details of bonding type rmsd covalent geometry : bond 0.00306 (28503) covalent geometry : angle 0.51291 (38889) hydrogen bonds : bond 0.03691 ( 1015) hydrogen bonds : angle 4.35351 ( 2890) metal coordination : bond 0.00390 ( 8) metal coordination : angle 2.70626 ( 12) *********************** 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 415 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 297 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6769 (ptt180) REVERT: A 232 ASP cc_start: 0.7923 (p0) cc_final: 0.7718 (p0) REVERT: A 379 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7312 (ttm-80) REVERT: B 22 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8502 (ttt-90) REVERT: B 212 GLN cc_start: 0.4457 (OUTLIER) cc_final: 0.4206 (tm-30) REVERT: B 240 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7705 (t70) REVERT: D 165 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.7832 (t) REVERT: D 222 ASP cc_start: 0.8648 (t70) cc_final: 0.8303 (t0) REVERT: E 76 GLU cc_start: 0.3259 (OUTLIER) cc_final: 0.2347 (pm20) REVERT: F 82 GLN cc_start: 0.4888 (OUTLIER) cc_final: 0.4201 (mp10) REVERT: F 367 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7773 (mm-30) REVERT: G 4 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8384 (mm-30) REVERT: G 76 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.4965 (pm20) REVERT: G 148 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8230 (tmm) REVERT: G 337 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.6817 (m-10) REVERT: G 352 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6405 (mp0) REVERT: H 4 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7964 (mm-30) REVERT: H 47 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8039 (ptt-90) REVERT: H 209 MET cc_start: 0.8794 (mtt) cc_final: 0.8577 (mtm) REVERT: I 298 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: J 230 THR cc_start: 0.8619 (m) cc_final: 0.8162 (p) REVERT: J 259 MET cc_start: 0.6472 (tpp) cc_final: 0.6030 (ttp) REVERT: J 262 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: J 319 GLU cc_start: 0.5932 (tm-30) cc_final: 0.5649 (tm-30) REVERT: J 441 ARG cc_start: 0.8097 (ptp-170) cc_final: 0.7856 (mtm-85) REVERT: J 445 LYS cc_start: 0.7153 (tttt) cc_final: 0.6407 (tttt) REVERT: K 92 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7277 (mt) outliers start: 118 outliers final: 67 residues processed: 392 average time/residue: 0.1783 time to fit residues: 108.9646 Evaluate side-chains 365 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 280 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 204 LEU 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 A residue 379 ARG Chi-restraints excluded: chain B residue 22 ARG Chi-restraints excluded: chain B residue 77 ASP 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 212 GLN Chi-restraints excluded: chain B residue 240 ASP 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 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 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 45 SER Chi-restraints excluded: chain F residue 82 GLN 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 4 GLU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 76 GLU 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 227 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 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 167 VAL Chi-restraints excluded: chain I residue 186 ILE 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 I residue 298 GLU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 108 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 151 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 250 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 243 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** A 312 ASN F 70 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 = 0.4010 r_free = 0.4010 target = 0.169666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124752 restraints weight = 36748.796| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.43 r_work: 0.3282 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 28511 Z= 0.270 Angle : 0.625 9.121 38901 Z= 0.324 Chirality : 0.045 0.232 4283 Planarity : 0.004 0.043 4830 Dihedral : 12.696 168.394 4559 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 4.93 % Allowed : 32.08 % Favored : 62.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.15), residues: 3337 helix: 0.48 (0.16), residues: 1156 sheet: 0.21 (0.22), residues: 542 loop : -1.67 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 60 TYR 0.020 0.002 TYR F 316 PHE 0.024 0.002 PHE D 102 TRP 0.016 0.002 TRP K 156 HIS 0.008 0.001 HIS I 204 Details of bonding type rmsd covalent geometry : bond 0.00640 (28503) covalent geometry : angle 0.62231 (38889) hydrogen bonds : bond 0.04824 ( 1015) hydrogen bonds : angle 4.68988 ( 2890) metal coordination : bond 0.00693 ( 8) metal coordination : angle 3.58167 ( 12) *********************** 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 425 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 286 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 289 GLU cc_start: 0.8500 (tp30) cc_final: 0.8193 (tp30) REVERT: D 165 THR cc_start: 0.8424 (p) cc_final: 0.7876 (t) REVERT: D 222 ASP cc_start: 0.8804 (t70) cc_final: 0.8491 (t0) REVERT: E 19 ASP cc_start: 0.8286 (t70) cc_final: 0.7994 (t70) REVERT: E 76 GLU cc_start: 0.3299 (OUTLIER) cc_final: 0.2431 (pm20) REVERT: E 171 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8629 (tp) REVERT: E 254 SER cc_start: 0.8672 (p) cc_final: 0.8394 (p) REVERT: F 82 GLN cc_start: 0.4659 (OUTLIER) cc_final: 0.3999 (mp10) REVERT: G 148 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8202 (tmm) REVERT: G 337 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6964 (m-10) REVERT: G 352 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6502 (mp0) REVERT: H 4 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: H 102 PHE cc_start: 0.8198 (t80) cc_final: 0.7775 (t80) REVERT: H 156 LYS cc_start: 0.3524 (OUTLIER) cc_final: 0.3101 (mtmt) REVERT: J 259 MET cc_start: 0.6632 (tpp) cc_final: 0.6076 (ttp) REVERT: J 262 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6589 (mp10) REVERT: J 319 GLU cc_start: 0.6021 (tm-30) cc_final: 0.5744 (tm-30) REVERT: J 418 ASN cc_start: 0.7178 (p0) cc_final: 0.6688 (p0) REVERT: J 445 LYS cc_start: 0.7250 (tttt) cc_final: 0.6705 (tttt) REVERT: K 92 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7344 (mt) REVERT: K 96 LYS cc_start: 0.7492 (mmtp) cc_final: 0.7229 (mmmm) outliers start: 139 outliers final: 86 residues processed: 401 average time/residue: 0.1722 time to fit residues: 108.3372 Evaluate side-chains 372 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 276 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 186 LEU 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 100 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 245 LEU Chi-restraints excluded: chain B residue 248 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 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 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 171 LEU Chi-restraints excluded: chain E residue 190 VAL 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 259 SER 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 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 129 VAL 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 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 227 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 352 GLU Chi-restraints excluded: chain G residue 365 LYS 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 17 ASN 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 71 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 293 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN D 70 GLN F 70 GLN I 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.173514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127887 restraints weight = 36408.203| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.66 r_work: 0.3326 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1248 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= 0.118 Angle : 0.523 8.886 38901 Z= 0.270 Chirality : 0.041 0.198 4283 Planarity : 0.004 0.043 4830 Dihedral : 12.558 166.718 4559 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.90 % Allowed : 32.72 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.15), residues: 3337 helix: 0.84 (0.16), residues: 1154 sheet: 0.37 (0.22), residues: 537 loop : -1.56 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 441 TYR 0.011 0.001 TYR A 283 PHE 0.014 0.001 PHE D 102 TRP 0.018 0.001 TRP K 156 HIS 0.007 0.001 HIS I 204 Details of bonding type rmsd covalent geometry : bond 0.00264 (28503) covalent geometry : angle 0.51888 (38889) hydrogen bonds : bond 0.03563 ( 1015) hydrogen bonds : angle 4.32765 ( 2890) metal coordination : bond 0.00580 ( 8) metal coordination : angle 3.79900 ( 12) *********************** 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 406 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 296 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6699 (ptt180) REVERT: A 232 ASP cc_start: 0.8188 (p0) cc_final: 0.7899 (p0) REVERT: D 67 LEU cc_start: 0.7960 (tp) cc_final: 0.6997 (mm) REVERT: D 165 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7811 (t) REVERT: D 222 ASP cc_start: 0.8670 (t70) cc_final: 0.8348 (t0) REVERT: E 76 GLU cc_start: 0.3185 (OUTLIER) cc_final: 0.2336 (pm20) REVERT: E 319 GLN cc_start: 0.7322 (tm-30) cc_final: 0.7099 (tm-30) REVERT: F 82 GLN cc_start: 0.4722 (OUTLIER) cc_final: 0.4047 (mp10) REVERT: G 76 GLU cc_start: 0.5277 (OUTLIER) cc_final: 0.4922 (pm20) REVERT: G 148 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8203 (tmm) REVERT: G 337 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6959 (m-10) REVERT: G 352 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: H 4 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: H 47 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7916 (ptt-90) REVERT: H 102 PHE cc_start: 0.8027 (t80) cc_final: 0.7785 (t80) REVERT: H 156 LYS cc_start: 0.3381 (OUTLIER) cc_final: 0.2788 (mtmt) REVERT: H 209 MET cc_start: 0.8826 (mtt) cc_final: 0.8621 (mtm) REVERT: J 230 THR cc_start: 0.8706 (m) cc_final: 0.8191 (p) REVERT: J 259 MET cc_start: 0.6474 (tpp) cc_final: 0.6114 (ttp) REVERT: J 262 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: J 319 GLU cc_start: 0.5916 (tm-30) cc_final: 0.5610 (tm-30) REVERT: J 418 ASN cc_start: 0.7119 (p0) cc_final: 0.6720 (p0) REVERT: J 445 LYS cc_start: 0.7269 (tttt) cc_final: 0.6790 (tttt) REVERT: K 92 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7302 (mt) REVERT: K 161 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7784 (mp) outliers start: 110 outliers final: 67 residues processed: 384 average time/residue: 0.1717 time to fit residues: 102.8528 Evaluate side-chains 360 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 279 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 77 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 128 GLN 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 332 ARG 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 75 THR 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 259 SER 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 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 76 GLU 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 148 MET Chi-restraints excluded: chain G residue 181 ILE 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 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 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 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 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 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 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 185 optimal weight: 0.0070 chunk 149 optimal weight: 30.0000 chunk 312 optimal weight: 9.9990 chunk 116 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 129 optimal weight: 0.0470 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.0370 overall best weight: 1.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.174726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128974 restraints weight = 36337.772| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.61 r_work: 0.3345 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.002 0.038 28511 Z= 0.105 Angle : 0.507 9.200 38901 Z= 0.260 Chirality : 0.040 0.175 4283 Planarity : 0.003 0.044 4830 Dihedral : 12.459 165.983 4559 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.01 % Allowed : 32.40 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.15), residues: 3337 helix: 0.95 (0.16), residues: 1171 sheet: 0.50 (0.22), residues: 537 loop : -1.49 (0.16), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 363 TYR 0.012 0.001 TYR A 283 PHE 0.017 0.001 PHE D 102 TRP 0.017 0.001 TRP K 156 HIS 0.005 0.001 HIS I 204 Details of bonding type rmsd covalent geometry : bond 0.00234 (28503) covalent geometry : angle 0.50309 (38889) hydrogen bonds : bond 0.03329 ( 1015) hydrogen bonds : angle 4.18204 ( 2890) metal coordination : bond 0.00435 ( 8) metal coordination : angle 3.48499 ( 12) *********************** 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 407 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 294 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6774 (ptt180) REVERT: A 232 ASP cc_start: 0.8044 (p0) cc_final: 0.7798 (p0) REVERT: A 289 GLU cc_start: 0.8486 (tp30) cc_final: 0.7902 (tp30) REVERT: D 67 LEU cc_start: 0.7968 (tp) cc_final: 0.6903 (mm) REVERT: D 222 ASP cc_start: 0.8655 (t70) cc_final: 0.8312 (t0) REVERT: E 76 GLU cc_start: 0.3275 (OUTLIER) cc_final: 0.2397 (pm20) REVERT: F 82 GLN cc_start: 0.4790 (OUTLIER) cc_final: 0.4098 (mp10) REVERT: F 171 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9092 (tp) REVERT: G 148 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8263 (tmm) REVERT: G 337 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6832 (m-10) REVERT: G 352 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: H 4 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: H 47 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7856 (ptt-90) REVERT: H 295 ASP cc_start: 0.8238 (m-30) cc_final: 0.7967 (m-30) REVERT: J 230 THR cc_start: 0.8673 (m) cc_final: 0.8191 (p) REVERT: J 259 MET cc_start: 0.6433 (tpp) cc_final: 0.6170 (ttp) REVERT: J 262 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.7048 (mp10) REVERT: J 319 GLU cc_start: 0.5935 (tm-30) cc_final: 0.5619 (tm-30) REVERT: J 328 GLU cc_start: 0.6363 (pp20) cc_final: 0.6118 (pp20) REVERT: J 418 ASN cc_start: 0.7028 (p0) cc_final: 0.6647 (p0) REVERT: J 445 LYS cc_start: 0.7330 (tttt) cc_final: 0.6887 (tttt) REVERT: K 54 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8717 (mmm-85) REVERT: K 92 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7309 (mt) REVERT: K 124 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7492 (mtt) REVERT: K 161 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7763 (mp) outliers start: 113 outliers final: 75 residues processed: 387 average time/residue: 0.1767 time to fit residues: 107.1430 Evaluate side-chains 375 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 287 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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 186 LEU 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 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR 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 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 152 ASN Chi-restraints excluded: chain D residue 154 LYS 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 75 THR 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 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 18 ARG 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 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 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 251 THR 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 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 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 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 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 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 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 Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 288 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 230 optimal weight: 0.0060 chunk 324 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 278 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 325 optimal weight: 0.6980 chunk 226 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 overall best weight: 1.7402 ------------------------------------------------------------------------------- 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** A 312 ASN F 70 GLN F 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128615 restraints weight = 36537.594| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.42 r_work: 0.3336 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1303 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= 0.131 Angle : 0.521 8.701 38901 Z= 0.267 Chirality : 0.041 0.181 4283 Planarity : 0.003 0.040 4830 Dihedral : 12.428 166.205 4559 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.79 % Allowed : 32.72 % Favored : 63.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.15), residues: 3337 helix: 1.00 (0.16), residues: 1161 sheet: 0.49 (0.22), residues: 537 loop : -1.48 (0.16), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 441 TYR 0.013 0.001 TYR D 337 PHE 0.014 0.001 PHE D 102 TRP 0.018 0.001 TRP J 159 HIS 0.005 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00302 (28503) covalent geometry : angle 0.51762 (38889) hydrogen bonds : bond 0.03521 ( 1015) hydrogen bonds : angle 4.20583 ( 2890) metal coordination : bond 0.00431 ( 8) metal coordination : angle 3.32268 ( 12) *********************** 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 393 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 286 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.6786 (ptt180) REVERT: A 144 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: A 232 ASP cc_start: 0.8081 (p0) cc_final: 0.7780 (p0) REVERT: A 289 GLU cc_start: 0.8499 (tp30) cc_final: 0.7910 (tp30) REVERT: D 56 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6437 (tp) REVERT: D 222 ASP cc_start: 0.8697 (t70) cc_final: 0.8349 (t0) REVERT: E 76 GLU cc_start: 0.3290 (OUTLIER) cc_final: 0.2394 (pm20) REVERT: F 82 GLN cc_start: 0.4779 (OUTLIER) cc_final: 0.4080 (mp10) REVERT: F 171 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9090 (tp) REVERT: G 148 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8289 (tmm) REVERT: G 337 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.6886 (m-10) REVERT: G 352 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6423 (mp0) REVERT: H 4 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7971 (mm-30) REVERT: H 47 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7903 (ptt-90) REVERT: H 295 ASP cc_start: 0.8326 (m-30) cc_final: 0.8045 (m-30) REVERT: J 230 THR cc_start: 0.8677 (m) cc_final: 0.8180 (p) REVERT: J 259 MET cc_start: 0.6446 (tpp) cc_final: 0.6155 (ttp) REVERT: J 262 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: J 319 GLU cc_start: 0.6030 (tm-30) cc_final: 0.5715 (tm-30) REVERT: J 328 GLU cc_start: 0.6335 (pp20) cc_final: 0.6104 (pp20) REVERT: J 418 ASN cc_start: 0.7035 (p0) cc_final: 0.6687 (p0) REVERT: J 441 ARG cc_start: 0.7997 (mtm110) cc_final: 0.7593 (ptp-170) REVERT: J 445 LYS cc_start: 0.7423 (tttt) cc_final: 0.6977 (tttt) REVERT: K 54 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8721 (mmm-85) REVERT: K 92 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7277 (mt) REVERT: K 124 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: K 161 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7774 (mp) outliers start: 107 outliers final: 81 residues processed: 374 average time/residue: 0.1754 time to fit residues: 102.7821 Evaluate side-chains 377 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 281 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 144 GLU 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 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 77 ASP 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 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 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 152 ASN Chi-restraints excluded: chain D residue 154 LYS 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 75 THR 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 259 SER 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 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 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 251 THR 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 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 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 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 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU 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 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 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 137 optimal weight: 0.2980 chunk 305 optimal weight: 0.0970 chunk 91 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 266 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 248 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.172802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127247 restraints weight = 36470.936| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.51 r_work: 0.3325 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1331 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= 0.156 Angle : 0.537 8.530 38901 Z= 0.277 Chirality : 0.041 0.191 4283 Planarity : 0.004 0.039 4830 Dihedral : 12.453 166.957 4559 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.76 % Allowed : 32.97 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.15), residues: 3337 helix: 0.96 (0.16), residues: 1157 sheet: 0.41 (0.22), residues: 545 loop : -1.49 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 363 TYR 0.013 0.001 TYR B 29 PHE 0.019 0.001 PHE D 102 TRP 0.020 0.001 TRP J 159 HIS 0.005 0.001 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00363 (28503) covalent geometry : angle 0.53329 (38889) hydrogen bonds : bond 0.03765 ( 1015) hydrogen bonds : angle 4.27873 ( 2890) metal coordination : bond 0.00486 ( 8) metal coordination : angle 3.50308 ( 12) *********************** 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 393 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 287 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6691 (ptt180) REVERT: A 144 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: A 232 ASP cc_start: 0.8166 (p0) cc_final: 0.7837 (p0) REVERT: D 56 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6427 (tp) REVERT: D 67 LEU cc_start: 0.7872 (tp) cc_final: 0.6822 (mm) REVERT: D 78 TRP cc_start: 0.7029 (OUTLIER) cc_final: 0.5777 (t60) REVERT: D 165 THR cc_start: 0.8288 (p) cc_final: 0.7769 (t) REVERT: D 222 ASP cc_start: 0.8715 (t70) cc_final: 0.8343 (t0) REVERT: E 76 GLU cc_start: 0.3236 (OUTLIER) cc_final: 0.2343 (pm20) REVERT: E 319 GLN cc_start: 0.7277 (tm-30) cc_final: 0.7066 (tm-30) REVERT: F 82 GLN cc_start: 0.4653 (OUTLIER) cc_final: 0.3970 (mp10) REVERT: F 171 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9098 (tp) REVERT: G 76 GLU cc_start: 0.5368 (OUTLIER) cc_final: 0.5004 (pm20) REVERT: G 148 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8218 (tmm) REVERT: G 337 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: G 352 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: H 4 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7863 (mm-30) REVERT: H 47 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7928 (ptt-90) REVERT: H 156 LYS cc_start: 0.3517 (OUTLIER) cc_final: 0.2992 (mtmt) REVERT: H 295 ASP cc_start: 0.8340 (m-30) cc_final: 0.8064 (m-30) REVERT: J 230 THR cc_start: 0.8705 (m) cc_final: 0.8195 (p) REVERT: J 259 MET cc_start: 0.6487 (tpp) cc_final: 0.6209 (ttp) REVERT: J 262 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: J 319 GLU cc_start: 0.6027 (tm-30) cc_final: 0.5714 (tm-30) REVERT: J 418 ASN cc_start: 0.6977 (p0) cc_final: 0.6615 (p0) REVERT: J 445 LYS cc_start: 0.7436 (tttt) cc_final: 0.7006 (tttt) REVERT: K 92 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7255 (mt) REVERT: K 124 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.7631 (mtt) outliers start: 106 outliers final: 83 residues processed: 377 average time/residue: 0.1773 time to fit residues: 104.1693 Evaluate side-chains 383 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 283 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 144 GLU 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 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 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 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 90 PHE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS 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 56 LEU Chi-restraints excluded: chain E residue 75 THR 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 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 82 GLN Chi-restraints excluded: chain F residue 171 LEU 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 76 GLU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 251 THR 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 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 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 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 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 137 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 127 optimal weight: 0.0980 chunk 209 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 70 GLN I 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.174272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.128577 restraints weight = 36438.300| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.60 r_work: 0.3344 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1355 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= 0.115 Angle : 0.513 9.658 38901 Z= 0.264 Chirality : 0.040 0.179 4283 Planarity : 0.003 0.040 4830 Dihedral : 12.410 166.326 4559 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.72 % Allowed : 32.97 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.15), residues: 3337 helix: 1.02 (0.16), residues: 1169 sheet: 0.50 (0.22), residues: 537 loop : -1.47 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 60 TYR 0.015 0.001 TYR E 316 PHE 0.014 0.001 PHE D 102 TRP 0.022 0.001 TRP J 159 HIS 0.005 0.001 HIS I 204 Details of bonding type rmsd covalent geometry : bond 0.00261 (28503) covalent geometry : angle 0.50994 (38889) hydrogen bonds : bond 0.03386 ( 1015) hydrogen bonds : angle 4.16442 ( 2890) metal coordination : bond 0.00400 ( 8) metal coordination : angle 3.21032 ( 12) ********************** 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 395 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 290 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6750 (ptt180) REVERT: A 144 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.6318 (tm-30) REVERT: A 232 ASP cc_start: 0.8103 (p0) cc_final: 0.7819 (p0) REVERT: A 289 GLU cc_start: 0.8485 (tp30) cc_final: 0.7903 (tp30) REVERT: D 56 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6356 (tp) REVERT: D 67 LEU cc_start: 0.7907 (tp) cc_final: 0.6838 (mm) REVERT: D 78 TRP cc_start: 0.7046 (OUTLIER) cc_final: 0.5790 (t60) REVERT: D 222 ASP cc_start: 0.8671 (t70) cc_final: 0.8314 (t0) REVERT: E 76 GLU cc_start: 0.3183 (OUTLIER) cc_final: 0.2295 (pm20) REVERT: E 319 GLN cc_start: 0.7283 (tm-30) cc_final: 0.7060 (tm-30) REVERT: F 82 GLN cc_start: 0.4796 (OUTLIER) cc_final: 0.4082 (mp10) REVERT: F 171 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9100 (tp) REVERT: G 148 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8252 (tmm) REVERT: G 337 TYR cc_start: 0.7195 (OUTLIER) cc_final: 0.6906 (m-10) REVERT: G 352 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: H 4 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7969 (mm-30) REVERT: H 47 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7910 (ptt-90) REVERT: H 295 ASP cc_start: 0.8261 (m-30) cc_final: 0.7972 (m-30) REVERT: J 230 THR cc_start: 0.8663 (m) cc_final: 0.8169 (p) REVERT: J 259 MET cc_start: 0.6429 (tpp) cc_final: 0.6169 (ttp) REVERT: J 262 GLN cc_start: 0.7396 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: J 319 GLU cc_start: 0.5969 (tm-30) cc_final: 0.5648 (tm-30) REVERT: J 418 ASN cc_start: 0.6919 (p0) cc_final: 0.6571 (p0) REVERT: J 441 ARG cc_start: 0.7987 (mtm110) cc_final: 0.7579 (ptp-170) REVERT: J 445 LYS cc_start: 0.7459 (tttt) cc_final: 0.7044 (tttt) REVERT: K 54 ARG cc_start: 0.8924 (mmm160) cc_final: 0.8723 (mmm-85) REVERT: K 92 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7229 (mt) REVERT: K 124 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.7563 (mtt) REVERT: K 161 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7749 (mp) outliers start: 105 outliers final: 83 residues processed: 378 average time/residue: 0.2137 time to fit residues: 124.5012 Evaluate side-chains 382 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 283 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 144 GLU 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 258 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 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 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 90 PHE 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 210 PHE Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 291 VAL 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 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 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 82 GLN Chi-restraints excluded: chain F residue 171 LEU 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 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 251 THR 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 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 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 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 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU 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 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 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 240 optimal weight: 0.2980 chunk 235 optimal weight: 10.0000 chunk 287 optimal weight: 0.0570 chunk 208 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 261 optimal weight: 0.4980 chunk 307 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN H 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.177548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132820 restraints weight = 36298.950| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.36 r_work: 0.3396 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28511 Z= 0.089 Angle : 0.492 9.574 38901 Z= 0.251 Chirality : 0.039 0.162 4283 Planarity : 0.003 0.041 4830 Dihedral : 12.318 164.732 4559 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.08 % Allowed : 33.53 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 3337 helix: 1.23 (0.16), residues: 1163 sheet: 0.63 (0.22), residues: 527 loop : -1.44 (0.16), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 363 TYR 0.013 0.001 TYR E 316 PHE 0.011 0.001 PHE I 244 TRP 0.029 0.001 TRP F 162 HIS 0.003 0.000 HIS I 204 Details of bonding type rmsd covalent geometry : bond 0.00194 (28503) covalent geometry : angle 0.48920 (38889) hydrogen bonds : bond 0.02881 ( 1015) hydrogen bonds : angle 3.96841 ( 2890) metal coordination : bond 0.00305 ( 8) metal coordination : angle 3.07722 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8246.58 seconds wall clock time: 141 minutes 24.63 seconds (8484.63 seconds total)