Starting phenix.real_space_refine on Tue Aug 26 17:26:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qr1_18611/08_2025/8qr1_18611.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qr1_18611/08_2025/8qr1_18611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qr1_18611/08_2025/8qr1_18611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qr1_18611/08_2025/8qr1_18611.map" model { file = "/net/cci-nas-00/data/ceres_data/8qr1_18611/08_2025/8qr1_18611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qr1_18611/08_2025/8qr1_18611.cif" } resolution = 2.4 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= -0.003 sd= 1.069 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: 4 Type Number sf(0) Gaussians S 202 5.16 5 C 24852 2.51 5 N 6851 2.21 5 O 7448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.04s 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: 39353 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 7059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 875, 7059 Classifications: {'peptide': 875} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 832} Chain breaks: 4 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 1, 'GLU:plan': 7, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 74 Chain: "C" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "F" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1781 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 200} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "G" Number of atoms: 2764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2764 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 335} Chain breaks: 1 Chain: "K" Number of atoms: 3164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3164 Classifications: {'peptide': 406} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 383} Chain breaks: 1 Chain: "L" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3374 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 17, 'TRANS': 421} Chain: "H" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3299 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 418} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3329 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3362 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3383 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "J" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3403 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 11, 'TRANS': 427} Time building chain proxies: 7.87, per 1000 atoms: 0.20 Number of scatterers: 39353 At special positions: 0 Unit cell: (132.13, 193.45, 202.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 202 16.00 O 7448 8.00 N 6851 7.00 C 24852 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: 2.59 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 953.7 nanoseconds 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9370 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 48 sheets defined 48.3% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 777 through 791 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 900 removed outlier: 3.507A pdb=" N LYS A 851 " --> pdb=" O HIS A 847 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 852 " --> pdb=" O HIS A 848 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 873 " --> pdb=" O ILE A 869 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 874 " --> pdb=" O ALA A 870 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N GLU A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1068 Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 4.013A pdb=" N ALA A1073 " --> pdb=" O LYS A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1109 Processing helix chain 'A' and resid 1121 through 1137 removed outlier: 3.620A pdb=" N GLN A1125 " --> pdb=" O GLY A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.585A pdb=" N TRP A1155 " --> pdb=" O ASN A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1185 Processing helix chain 'A' and resid 1197 through 1204 Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 3.889A pdb=" N ARG A1210 " --> pdb=" O THR A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1238 removed outlier: 3.535A pdb=" N TRP A1232 " --> pdb=" O THR A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1266 removed outlier: 3.560A pdb=" N VAL A1266 " --> pdb=" O VAL A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1285 through 1301 Processing helix chain 'A' and resid 1329 through 1342 Processing helix chain 'A' and resid 1342 through 1352 Processing helix chain 'A' and resid 1353 through 1370 Processing helix chain 'A' and resid 1371 through 1374 Processing helix chain 'A' and resid 1393 through 1397 removed outlier: 3.571A pdb=" N ILE A1396 " --> pdb=" O ALA A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 removed outlier: 3.815A pdb=" N GLU A1407 " --> pdb=" O PHE A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1414 Processing helix chain 'A' and resid 1422 through 1431 removed outlier: 5.205A pdb=" N GLU A1428 " --> pdb=" O ARG A1424 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1429 " --> pdb=" O HIS A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1758 removed outlier: 3.628A pdb=" N LEU A1755 " --> pdb=" O ASP A1751 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1832 removed outlier: 4.048A pdb=" N VAL A1827 " --> pdb=" O SER A1823 " (cutoff:3.500A) Processing helix chain 'A' and resid 1851 through 1870 Processing helix chain 'A' and resid 1872 through 1881 Processing helix chain 'A' and resid 1890 through 1896 removed outlier: 4.210A pdb=" N GLN A1894 " --> pdb=" O LEU A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 1897 through 1913 removed outlier: 3.716A pdb=" N ILE A1905 " --> pdb=" O GLU A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1937 removed outlier: 3.548A pdb=" N LEU A1927 " --> pdb=" O MET A1923 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET A1932 " --> pdb=" O ASP A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1963 Processing helix chain 'A' and resid 1974 through 1976 No H-bonds generated for 'chain 'A' and resid 1974 through 1976' Processing helix chain 'A' and resid 1996 through 2009 removed outlier: 3.512A pdb=" N ASP A2000 " --> pdb=" O ASN A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2026 through 2034 removed outlier: 3.637A pdb=" N ASN A2034 " --> pdb=" O LYS A2030 " (cutoff:3.500A) Processing helix chain 'A' and resid 2036 through 2041 removed outlier: 3.540A pdb=" N ILE A2040 " --> pdb=" O THR A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2047 Processing helix chain 'A' and resid 2048 through 2051 Processing helix chain 'A' and resid 2056 through 2064 Processing helix chain 'A' and resid 2189 through 2215 Processing helix chain 'A' and resid 2225 through 2229 Processing helix chain 'A' and resid 2265 through 2269 Processing helix chain 'C' and resid 399 through 403 removed outlier: 3.622A pdb=" N ALA C 403 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 461 through 463 No H-bonds generated for 'chain 'C' and resid 461 through 463' Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 118 through 120 No H-bonds generated for 'chain 'F' and resid 118 through 120' Processing helix chain 'F' and resid 124 through 130 Processing helix chain 'F' and resid 139 through 144 removed outlier: 3.676A pdb=" N GLN F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 Processing helix chain 'F' and resid 170 through 178 Processing helix chain 'F' and resid 179 through 184 Processing helix chain 'F' and resid 189 through 208 removed outlier: 3.740A pdb=" N TYR F 195 " --> pdb=" O LEU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 235 removed outlier: 3.586A pdb=" N GLU F 223 " --> pdb=" O ASP F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 256 Processing helix chain 'S' and resid 272 through 278 removed outlier: 4.042A pdb=" N GLU S 276 " --> pdb=" O ALA S 272 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP S 277 " --> pdb=" O THR S 273 " (cutoff:3.500A) Processing helix chain 'S' and resid 312 through 322 Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.873A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 78 through 92 removed outlier: 4.029A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.766A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 196 removed outlier: 3.620A pdb=" N LEU B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 263 Proline residue: B 258 - end of helix removed outlier: 3.618A pdb=" N PHE B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 273 through 285 removed outlier: 3.738A pdb=" N CYS B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 349 through 354 removed outlier: 4.085A pdb=" N PHE B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 349 through 354' Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.703A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.629A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 3.841A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 197 Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.595A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.716A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 284 Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.335A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.526A pdb=" N LEU G 349 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 356 removed outlier: 3.976A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP G 356 " --> pdb=" O GLN G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 3.502A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 76 removed outlier: 4.281A pdb=" N ALA K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 110 Processing helix chain 'K' and resid 114 through 118 removed outlier: 3.560A pdb=" N LEU K 117 " --> pdb=" O GLU K 114 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS K 118 " --> pdb=" O ALA K 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 114 through 118' Processing helix chain 'K' and resid 129 through 143 Processing helix chain 'K' and resid 154 through 162 removed outlier: 3.706A pdb=" N ASN K 162 " --> pdb=" O THR K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 192 Processing helix chain 'K' and resid 198 through 213 Processing helix chain 'K' and resid 219 through 221 No H-bonds generated for 'chain 'K' and resid 219 through 221' Processing helix chain 'K' and resid 247 through 267 removed outlier: 3.613A pdb=" N LEU K 267 " --> pdb=" O GLN K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 removed outlier: 3.665A pdb=" N GLN K 281 " --> pdb=" O GLN K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 304 Processing helix chain 'K' and resid 305 through 309 Processing helix chain 'K' and resid 310 through 314 removed outlier: 3.603A pdb=" N ASN K 313 " --> pdb=" O ASP K 310 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'K' and resid 340 through 346 Processing helix chain 'K' and resid 352 through 357 removed outlier: 3.644A pdb=" N ILE K 357 " --> pdb=" O ASN K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 372 Processing helix chain 'K' and resid 385 through 391 Processing helix chain 'K' and resid 391 through 403 Processing helix chain 'K' and resid 404 through 409 removed outlier: 4.081A pdb=" N GLN K 408 " --> pdb=" O THR K 405 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 420 Processing helix chain 'K' and resid 422 through 428 removed outlier: 4.115A pdb=" N ARG K 426 " --> pdb=" O GLN K 422 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 59 removed outlier: 3.928A pdb=" N LYS L 59 " --> pdb=" O LEU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 88 Processing helix chain 'L' and resid 99 through 102 Processing helix chain 'L' and resid 107 through 119 Processing helix chain 'L' and resid 173 through 183 Processing helix chain 'L' and resid 239 through 242 removed outlier: 3.967A pdb=" N ASP L 242 " --> pdb=" O THR L 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 239 through 242' Processing helix chain 'L' and resid 243 through 249 removed outlier: 3.572A pdb=" N ASN L 247 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG L 249 " --> pdb=" O VAL L 245 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 262 Processing helix chain 'L' and resid 272 through 289 Processing helix chain 'L' and resid 303 through 307 Processing helix chain 'L' and resid 308 through 320 removed outlier: 4.029A pdb=" N ARG L 317 " --> pdb=" O THR L 313 " (cutoff:3.500A) Processing helix chain 'L' and resid 347 through 350 Processing helix chain 'L' and resid 351 through 356 Processing helix chain 'L' and resid 367 through 382 Processing helix chain 'L' and resid 387 through 401 Processing helix chain 'L' and resid 402 through 409 Processing helix chain 'L' and resid 409 through 420 Processing helix chain 'L' and resid 426 through 437 removed outlier: 3.551A pdb=" N VAL L 430 " --> pdb=" O GLU L 426 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 450 Processing helix chain 'H' and resid 49 through 66 Processing helix chain 'H' and resid 82 through 95 Processing helix chain 'H' and resid 106 through 109 removed outlier: 3.538A pdb=" N PHE H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 109' Processing helix chain 'H' and resid 114 through 126 removed outlier: 3.704A pdb=" N SER H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 183 removed outlier: 4.090A pdb=" N LEU H 182 " --> pdb=" O MET H 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR H 183 " --> pdb=" O ILE H 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 178 through 183' Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 244 through 252 Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 269 through 286 removed outlier: 3.652A pdb=" N ARG H 273 " --> pdb=" O LYS H 269 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 304 Processing helix chain 'H' and resid 305 through 316 removed outlier: 3.842A pdb=" N ARG H 314 " --> pdb=" O SER H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 352 Processing helix chain 'H' and resid 363 through 378 Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 398 through 416 removed outlier: 3.659A pdb=" N ILE H 406 " --> pdb=" O ALA H 402 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA H 408 " --> pdb=" O GLN H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 433 Processing helix chain 'H' and resid 435 through 446 removed outlier: 3.545A pdb=" N GLN H 441 " --> pdb=" O SER H 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.956A pdb=" N LYS I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 99 through 102 removed outlier: 3.501A pdb=" N TYR I 102 " --> pdb=" O SER I 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 102' Processing helix chain 'I' and resid 107 through 119 removed outlier: 3.615A pdb=" N ALA I 119 " --> pdb=" O ASN I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 183 removed outlier: 4.072A pdb=" N GLU I 183 " --> pdb=" O SER I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 213 removed outlier: 4.520A pdb=" N THR I 211 " --> pdb=" O THR I 208 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU I 212 " --> pdb=" O TYR I 209 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE I 213 " --> pdb=" O ALA I 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 208 through 213' Processing helix chain 'I' and resid 240 through 249 Processing helix chain 'I' and resid 255 through 263 Processing helix chain 'I' and resid 272 through 289 removed outlier: 3.584A pdb=" N ARG I 276 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 307 Processing helix chain 'I' and resid 308 through 320 removed outlier: 3.619A pdb=" N HIS I 316 " --> pdb=" O PHE I 312 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ARG I 317 " --> pdb=" O THR I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 347 through 350 Processing helix chain 'I' and resid 351 through 357 removed outlier: 3.786A pdb=" N ARG I 357 " --> pdb=" O ASP I 353 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 383 Processing helix chain 'I' and resid 387 through 401 Processing helix chain 'I' and resid 402 through 409 removed outlier: 3.503A pdb=" N LEU I 409 " --> pdb=" O TYR I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 420 Processing helix chain 'I' and resid 426 through 437 removed outlier: 3.517A pdb=" N VAL I 430 " --> pdb=" O GLU I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 439 through 449 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 Processing helix chain 'D' and resid 106 through 109 removed outlier: 3.537A pdb=" N PHE D 109 " --> pdb=" O SER D 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 106 through 109' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.677A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 186 Processing helix chain 'D' and resid 244 through 253 removed outlier: 4.316A pdb=" N ARG D 253 " --> pdb=" O VAL D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.652A pdb=" N ARG D 273 " --> pdb=" O LYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.803A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 379 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.664A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.753A pdb=" N LYS E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 removed outlier: 3.541A pdb=" N ALA E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 102 removed outlier: 3.715A pdb=" N TYR E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 102' Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'E' and resid 175 through 183 removed outlier: 4.516A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 240 through 249 removed outlier: 3.892A pdb=" N ARG E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 264 removed outlier: 3.787A pdb=" N MET E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN E 262 " --> pdb=" O SER E 258 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU E 263 " --> pdb=" O MET E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 289 removed outlier: 3.529A pdb=" N ARG E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 308 through 320 removed outlier: 4.022A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU E 320 " --> pdb=" O HIS E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 402 through 409 Processing helix chain 'E' and resid 409 through 420 Processing helix chain 'E' and resid 426 through 437 removed outlier: 3.702A pdb=" N VAL E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU E 435 " --> pdb=" O GLU E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 450 removed outlier: 3.695A pdb=" N ALA E 448 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP E 449 " --> pdb=" O LYS E 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 66 Processing helix chain 'J' and resid 82 through 95 Processing helix chain 'J' and resid 106 through 109 Processing helix chain 'J' and resid 114 through 126 removed outlier: 3.510A pdb=" N SER J 126 " --> pdb=" O ALA J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 157 removed outlier: 3.693A pdb=" N GLY J 155 " --> pdb=" O THR J 152 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS J 157 " --> pdb=" O THR J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 185 Processing helix chain 'J' and resid 244 through 252 Processing helix chain 'J' and resid 256 through 263 removed outlier: 3.592A pdb=" N LEU J 260 " --> pdb=" O GLY J 256 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE J 261 " --> pdb=" O PHE J 257 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 286 removed outlier: 3.516A pdb=" N ARG J 273 " --> pdb=" O LYS J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 301 through 304 Processing helix chain 'J' and resid 305 through 316 removed outlier: 3.808A pdb=" N ARG J 314 " --> pdb=" O SER J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 352 Processing helix chain 'J' and resid 363 through 379 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 398 through 416 removed outlier: 3.630A pdb=" N ILE J 406 " --> pdb=" O ALA J 402 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA J 408 " --> pdb=" O GLN J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 433 removed outlier: 3.530A pdb=" N ILE J 426 " --> pdb=" O GLN J 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 435 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 801 through 802 Processing sheet with id=AA2, first strand: chain 'A' and resid 1168 through 1170 removed outlier: 3.783A pdb=" N LEU A1169 " --> pdb=" O VAL A1193 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE A1195 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N CYS A1194 " --> pdb=" O HIS A1143 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A1145 " --> pdb=" O CYS A1194 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR A1196 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU A1144 " --> pdb=" O CYS A1215 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A1217 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A1146 " --> pdb=" O VAL A1217 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU A1216 " --> pdb=" O GLN A1242 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1321 through 1326 removed outlier: 6.317A pdb=" N VAL A1988 " --> pdb=" O TYR A2019 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N LEU A2021 " --> pdb=" O VAL A1988 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE A1990 " --> pdb=" O LEU A2021 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N SER A2023 " --> pdb=" O PHE A1990 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A1918 " --> pdb=" O VAL A1989 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A1942 " --> pdb=" O ILE A1970 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N SER A1972 " --> pdb=" O VAL A1942 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ILE A1944 " --> pdb=" O SER A1972 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1390 through 1391 removed outlier: 6.534A pdb=" N TYR A1390 " --> pdb=" O ARG A1846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 2222 through 2224 Processing sheet with id=AA6, first strand: chain 'A' and resid 2234 through 2237 removed outlier: 4.894A pdb=" N ASP A2237 " --> pdb=" O GLN A2241 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN A2241 " --> pdb=" O ASP A2237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 2247 through 2248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2247 through 2248 current: chain 'C' and resid 451 through 459 Processing sheet with id=AA8, first strand: chain 'F' and resid 95 through 100 Processing sheet with id=AA9, first strand: chain 'S' and resid 214 through 216 removed outlier: 3.801A pdb=" N TYR S 214 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N VAL D 142 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS D 164 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL D 158 " --> pdb=" O ASP D 148 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLY D 159 " --> pdb=" O LEU D 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 169 through 174 current: chain 'D' and resid 202 through 207 Processing sheet with id=AB1, first strand: chain 'B' and resid 29 through 30 removed outlier: 4.085A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 19 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS B 18 " --> pdb=" O ASP B 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 11 " --> pdb=" O LYS B 18 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 20 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 9 " --> pdb=" O GLY B 20 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA B 135 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'B' and resid 150 through 155 removed outlier: 3.709A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 240 through 241 removed outlier: 3.917A pdb=" N TYR B 240 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE B 248 " --> pdb=" O TYR B 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 29 through 32 removed outlier: 6.600A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N VAL G 10 " --> pdb=" O THR G 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'G' and resid 150 through 155 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 169 through 170 current: chain 'G' and resid 329 through 330 Processing sheet with id=AB8, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'K' and resid 35 through 38 removed outlier: 6.372A pdb=" N LEU K 14 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER K 123 " --> pdb=" O LEU K 14 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE K 16 " --> pdb=" O SER K 123 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL K 120 " --> pdb=" O PHE K 150 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N CYS K 152 " --> pdb=" O VAL K 120 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N MET K 122 " --> pdb=" O CYS K 152 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 67 through 69 Processing sheet with id=AC2, first strand: chain 'K' and resid 88 through 89 Processing sheet with id=AC3, first strand: chain 'K' and resid 167 through 172 Processing sheet with id=AC4, first strand: chain 'K' and resid 223 through 227 removed outlier: 6.739A pdb=" N LYS K 238 " --> pdb=" O ALA K 224 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS K 226 " --> pdb=" O ASN K 236 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN K 236 " --> pdb=" O LYS K 226 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 285 through 288 Processing sheet with id=AC6, first strand: chain 'L' and resid 35 through 36 Processing sheet with id=AC7, first strand: chain 'L' and resid 93 through 97 removed outlier: 6.523A pdb=" N CYS L 94 " --> pdb=" O PHE L 300 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP L 302 " --> pdb=" O CYS L 94 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N MET L 96 " --> pdb=" O ASP L 302 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL L 66 " --> pdb=" O PHE L 329 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER L 331 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU L 68 " --> pdb=" O SER L 331 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA L 65 " --> pdb=" O MET L 359 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE L 361 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU L 67 " --> pdb=" O ILE L 361 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 120 through 137 removed outlier: 6.533A pdb=" N GLY L 160 " --> pdb=" O THR L 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 167 through 171 current: chain 'L' and resid 200 through 205 Processing sheet with id=AC9, first strand: chain 'L' and resid 336 through 337 Processing sheet with id=AD1, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AD2, first strand: chain 'H' and resid 100 through 104 removed outlier: 6.412A pdb=" N THR H 101 " --> pdb=" O PHE H 297 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ASP H 299 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE H 103 " --> pdb=" O ASP H 299 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU H 296 " --> pdb=" O ILE H 325 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ALA H 327 " --> pdb=" O LEU H 296 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE H 298 " --> pdb=" O ALA H 327 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY H 77 " --> pdb=" O THR H 328 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ALA H 72 " --> pdb=" O LEU H 355 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL H 357 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU H 74 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR H 359 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA H 76 " --> pdb=" O THR H 359 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 127 through 142 Processing sheet with id=AD4, first strand: chain 'H' and resid 332 through 334 Processing sheet with id=AD5, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AD6, first strand: chain 'I' and resid 93 through 97 removed outlier: 6.581A pdb=" N CYS I 94 " --> pdb=" O PHE I 300 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASP I 302 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N MET I 96 " --> pdb=" O ASP I 302 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA I 65 " --> pdb=" O MET I 359 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ILE I 361 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU I 67 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 120 through 143 removed outlier: 5.862A pdb=" N VAL I 135 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS I 162 " --> pdb=" O VAL I 135 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU I 137 " --> pdb=" O GLY I 160 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR I 143 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE I 154 " --> pdb=" O THR I 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 172 current: chain 'I' and resid 199 through 206 removed outlier: 5.846A pdb=" N VAL I 221 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG I 205 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 336 through 337 Processing sheet with id=AD9, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AE1, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.393A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AE3, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AE4, first strand: chain 'E' and resid 93 through 97 removed outlier: 6.400A pdb=" N CYS E 94 " --> pdb=" O PHE E 300 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ASP E 302 " --> pdb=" O CYS E 94 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N MET E 96 " --> pdb=" O ASP E 302 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 236 through 239 Processing sheet with id=AE6, first strand: chain 'E' and resid 127 through 135 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 127 through 135 current: chain 'E' and resid 157 through 162 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 172 current: chain 'E' and resid 200 through 205 Processing sheet with id=AE7, first strand: chain 'E' and resid 335 through 337 Processing sheet with id=AE8, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AE9, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.232A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 236 through 243 removed outlier: 3.713A pdb=" N LYS J 236 " --> pdb=" O THR J 135 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 169 through 173 removed outlier: 6.750A pdb=" N LYS J 160 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE J 145 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP J 191 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR J 194 " --> pdb=" O LYS J 204 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LYS J 204 " --> pdb=" O THR J 194 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ASP J 196 " --> pdb=" O ILE J 202 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE J 202 " --> pdb=" O ASP J 196 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 332 through 334 1668 hydrogen bonds defined for protein. 4749 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.08 Time building geometry restraints manager: 3.57 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: 12997 1.34 - 1.46: 7935 1.46 - 1.58: 18781 1.58 - 1.70: 0 1.70 - 1.82: 336 Bond restraints: 40049 Sorted by residual: bond pdb=" C GLU S 347 " pdb=" N PRO S 348 " ideal model delta sigma weight residual 1.332 1.381 -0.050 1.34e-02 5.57e+03 1.37e+01 bond pdb=" CA GLU E 212 " pdb=" CB GLU E 212 " ideal model delta sigma weight residual 1.530 1.566 -0.036 1.47e-02 4.63e+03 5.87e+00 bond pdb=" N GLY K 4 " pdb=" CA GLY K 4 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.64e+00 bond pdb=" CB ARG C 450 " pdb=" CG ARG C 450 " ideal model delta sigma weight residual 1.520 1.580 -0.060 3.00e-02 1.11e+03 4.05e+00 bond pdb=" CB ASP A1826 " pdb=" CG ASP A1826 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 3.93e+00 ... (remaining 40044 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 52499 2.25 - 4.49: 1259 4.49 - 6.74: 328 6.74 - 8.98: 30 8.98 - 11.23: 8 Bond angle restraints: 54124 Sorted by residual: angle pdb=" CA MET B 119 " pdb=" CB MET B 119 " pdb=" CG MET B 119 " ideal model delta sigma weight residual 114.10 124.80 -10.70 2.00e+00 2.50e-01 2.86e+01 angle pdb=" CA GLU E 212 " pdb=" CB GLU E 212 " pdb=" CG GLU E 212 " ideal model delta sigma weight residual 114.10 124.75 -10.65 2.00e+00 2.50e-01 2.84e+01 angle pdb=" CA PRO S 343 " pdb=" C PRO S 343 " pdb=" N PRO S 344 " ideal model delta sigma weight residual 117.93 124.24 -6.31 1.20e+00 6.94e-01 2.77e+01 angle pdb=" N PRO S 343 " pdb=" CA PRO S 343 " pdb=" C PRO S 343 " ideal model delta sigma weight residual 110.70 117.10 -6.40 1.22e+00 6.72e-01 2.76e+01 angle pdb=" CA ARG C 450 " pdb=" CB ARG C 450 " pdb=" CG ARG C 450 " ideal model delta sigma weight residual 114.10 123.64 -9.54 2.00e+00 2.50e-01 2.27e+01 ... (remaining 54119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 22117 17.89 - 35.77: 1804 35.77 - 53.66: 457 53.66 - 71.54: 107 71.54 - 89.43: 40 Dihedral angle restraints: 24525 sinusoidal: 9995 harmonic: 14530 Sorted by residual: dihedral pdb=" CA GLN C 449 " pdb=" C GLN C 449 " pdb=" N ARG C 450 " pdb=" CA ARG C 450 " ideal model delta harmonic sigma weight residual 180.00 141.72 38.28 0 5.00e+00 4.00e-02 5.86e+01 dihedral pdb=" CA ASP S 307 " pdb=" C ASP S 307 " pdb=" N ILE S 308 " pdb=" CA ILE S 308 " ideal model delta harmonic sigma weight residual 180.00 -147.70 -32.30 0 5.00e+00 4.00e-02 4.17e+01 dihedral pdb=" CA ASN F 102 " pdb=" C ASN F 102 " pdb=" N PRO F 103 " pdb=" CA PRO F 103 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 24522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4861 0.056 - 0.112: 1079 0.112 - 0.168: 205 0.168 - 0.225: 9 0.225 - 0.281: 3 Chirality restraints: 6157 Sorted by residual: chirality pdb=" CB VAL J 421 " pdb=" CA VAL J 421 " pdb=" CG1 VAL J 421 " pdb=" CG2 VAL J 421 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL A 841 " pdb=" CA VAL A 841 " pdb=" CG1 VAL A 841 " pdb=" CG2 VAL A 841 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE H 22 " pdb=" CA ILE H 22 " pdb=" CG1 ILE H 22 " pdb=" CG2 ILE H 22 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 6154 not shown) Planarity restraints: 6985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 215 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO F 216 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 216 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 216 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 211 " -0.267 9.50e-02 1.11e+02 1.20e-01 9.34e+00 pdb=" NE ARG D 211 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG D 211 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG D 211 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 211 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 102 " -0.050 5.00e-02 4.00e+02 7.61e-02 9.26e+00 pdb=" N PRO F 103 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO F 103 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 103 " -0.041 5.00e-02 4.00e+02 ... (remaining 6982 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 449 2.67 - 3.22: 36891 3.22 - 3.78: 58511 3.78 - 4.34: 82551 4.34 - 4.90: 135680 Nonbonded interactions: 314082 Sorted by model distance: nonbonded pdb=" O ARG B 62 " pdb=" OG1 THR B 203 " model vdw 2.107 3.040 nonbonded pdb=" O LEU A1205 " pdb=" OG1 THR A1209 " model vdw 2.175 3.040 nonbonded pdb=" OH TYR A1941 " pdb=" OD2 ASP I 207 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLN A1752 " pdb=" NZ LYS J 201 " model vdw 2.256 3.120 nonbonded pdb=" O LEU B 221 " pdb=" NZ LYS B 315 " model vdw 2.270 3.120 ... (remaining 314077 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 'B' and (resid 7 through 36 or resid 52 through 375)) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 15 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 156 through 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 through 210 or (resid 211 through 21 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 219 through \ 453)) selection = chain 'H' selection = (chain 'J' and (resid 15 through 148 or (resid 149 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 156 through 157 and (name N or name CA or \ name C or name O or name CB )) or resid 158 through 210 or (resid 211 through 21 \ 4 and (name N or name CA or name C or name O or name CB )) or resid 219 or (resi \ d 220 through 223 and (name N or name CA or name C or name O or name CB )) or re \ sid 224 through 453)) } ncs_group { reference = (chain 'E' and (resid 12 through 142 or (resid 143 through 145 and (name N or na \ me CA or name C or name O or name CB )) or (resid 152 through 153 and (name N or \ name CA or name C or name O or name CB )) or resid 154 through 450)) selection = (chain 'I' and resid 12 through 450) selection = (chain 'L' and (resid 12 through 142 or (resid 143 through 145 and (name N or na \ me CA or name C or name O or name CB )) or (resid 152 through 153 and (name N or \ name CA or name C or name O or name CB )) or resid 154 through 450)) } 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: 28.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.750 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 30.740 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 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 : 0.006 0.082 40049 Z= 0.250 Angle : 0.899 11.230 54124 Z= 0.478 Chirality : 0.048 0.281 6157 Planarity : 0.006 0.120 6985 Dihedral : 14.781 89.431 15155 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.63 % Favored : 96.09 % Rotamer: Outliers : 0.66 % Allowed : 10.12 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.09 (0.11), residues: 4983 helix: 0.61 (0.11), residues: 2120 sheet: -0.01 (0.18), residues: 690 loop : -0.33 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 211 TYR 0.025 0.002 TYR G 53 PHE 0.047 0.002 PHE E 177 TRP 0.014 0.001 TRP K 410 HIS 0.006 0.001 HIS C 416 Details of bonding type rmsd covalent geometry : bond 0.00622 (40049) covalent geometry : angle 0.89875 (54124) hydrogen bonds : bond 0.16595 ( 1668) hydrogen bonds : angle 5.77717 ( 4749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 351 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 HIS cc_start: 0.8509 (m-70) cc_final: 0.8218 (m90) REVERT: B 132 MET cc_start: 0.7935 (tpt) cc_final: 0.7432 (ttp) REVERT: B 153 MET cc_start: 0.8969 (tpt) cc_final: 0.8540 (mpp) REVERT: B 161 HIS cc_start: 0.8663 (m-70) cc_final: 0.8331 (t-90) REVERT: L 147 MET cc_start: 0.4344 (mpt) cc_final: 0.0514 (ptm) REVERT: H 112 GLU cc_start: 0.8610 (tp30) cc_final: 0.8406 (tp30) REVERT: D 34 ASP cc_start: 0.7958 (t0) cc_final: 0.7682 (t0) REVERT: D 211 ARG cc_start: 0.7996 (mtp-110) cc_final: 0.7709 (mtm110) REVERT: D 414 ARG cc_start: 0.8527 (ttm110) cc_final: 0.7895 (mmt180) REVERT: E 177 PHE cc_start: 0.8483 (p90) cc_final: 0.8239 (p90) REVERT: E 181 GLN cc_start: 0.9235 (mt0) cc_final: 0.8913 (pm20) REVERT: E 264 MET cc_start: 0.7987 (ptm) cc_final: 0.7456 (ppp) REVERT: J 288 LYS cc_start: 0.8990 (tttm) cc_final: 0.8622 (ttpm) outliers start: 28 outliers final: 19 residues processed: 375 average time/residue: 0.7331 time to fit residues: 330.4973 Evaluate side-chains 333 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 314 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain G residue 205 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 24 ARG Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain J residue 275 GLN Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 494 optimal weight: 0.5980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 811 HIS A1353 HIS F 175 HIS F 235 ASN G 12 ASN G 92 ASN G 314 GLN K 263 GLN L 34 GLN L 229 HIS L 241 HIS L 420 ASN H 313 ASN D 27 HIS D 313 ASN E 181 GLN E 429 HIS J 226 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.140836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.080837 restraints weight = 65207.185| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.99 r_work: 0.2903 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40049 Z= 0.139 Angle : 0.549 8.646 54124 Z= 0.287 Chirality : 0.043 0.171 6157 Planarity : 0.004 0.064 6985 Dihedral : 5.264 70.333 5507 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.21 % Favored : 96.53 % Rotamer: Outliers : 1.74 % Allowed : 9.69 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.72 (0.12), residues: 4983 helix: 1.25 (0.11), residues: 2139 sheet: 0.07 (0.18), residues: 750 loop : -0.04 (0.14), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 297 TYR 0.019 0.001 TYR F 246 PHE 0.013 0.001 PHE F 47 TRP 0.034 0.001 TRP B 86 HIS 0.004 0.001 HIS E 156 Details of bonding type rmsd covalent geometry : bond 0.00319 (40049) covalent geometry : angle 0.54862 (54124) hydrogen bonds : bond 0.04240 ( 1668) hydrogen bonds : angle 4.38852 ( 4749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 330 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1872 TYR cc_start: 0.7601 (m-80) cc_final: 0.7111 (m-10) REVERT: C 480 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.6297 (p-80) REVERT: F 202 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7668 (mt) REVERT: S 214 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.6839 (t80) REVERT: S 314 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8793 (tmm-80) REVERT: S 317 LYS cc_start: 0.8810 (tppt) cc_final: 0.8468 (ptmt) REVERT: S 318 ILE cc_start: 0.9320 (mm) cc_final: 0.8992 (mm) REVERT: B 16 MET cc_start: 0.6232 (pmm) cc_final: 0.5962 (pmm) REVERT: B 101 HIS cc_start: 0.7936 (m-70) cc_final: 0.7589 (m90) REVERT: B 153 MET cc_start: 0.8299 (tpt) cc_final: 0.8074 (mpp) REVERT: B 325 MET cc_start: -0.2458 (OUTLIER) cc_final: -0.2697 (ttp) REVERT: L 240 LEU cc_start: 0.3996 (OUTLIER) cc_final: 0.3680 (pt) REVERT: H 112 GLU cc_start: 0.8643 (tp30) cc_final: 0.8344 (tp30) REVERT: D 184 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8574 (mmtm) REVERT: D 211 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7729 (mtm180) REVERT: E 181 GLN cc_start: 0.9029 (mt0) cc_final: 0.8439 (mt0) REVERT: E 220 TYR cc_start: 0.8568 (m-80) cc_final: 0.8058 (m-10) REVERT: J 130 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: J 168 MET cc_start: 0.7960 (ttm) cc_final: 0.7591 (ttm) REVERT: J 204 LYS cc_start: 0.8272 (tptt) cc_final: 0.7988 (tptp) REVERT: J 248 ASP cc_start: 0.8638 (m-30) cc_final: 0.8391 (m-30) REVERT: J 288 LYS cc_start: 0.8566 (tttm) cc_final: 0.8060 (ttpm) outliers start: 74 outliers final: 29 residues processed: 375 average time/residue: 0.6739 time to fit residues: 305.0844 Evaluate side-chains 342 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 306 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 480 HIS Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain S residue 214 TYR Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 314 ARG Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain H residue 407 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 304 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 235 ARG Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 394 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 214 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 chunk 365 optimal weight: 4.9990 chunk 349 optimal weight: 0.8980 chunk 245 optimal weight: 0.5980 chunk 372 optimal weight: 0.6980 chunk 278 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 175 HIS F 204 ASN B 161 HIS I 181 GLN I 420 ASN J 27 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.140714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.080261 restraints weight = 65293.160| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 3.01 r_work: 0.2896 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40049 Z= 0.120 Angle : 0.510 7.734 54124 Z= 0.267 Chirality : 0.042 0.170 6157 Planarity : 0.004 0.058 6985 Dihedral : 4.863 69.429 5492 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.27 % Favored : 96.47 % Rotamer: Outliers : 1.84 % Allowed : 10.45 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 0.92 (0.12), residues: 4983 helix: 1.47 (0.11), residues: 2148 sheet: 0.21 (0.18), residues: 742 loop : -0.02 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 297 TYR 0.015 0.001 TYR A2223 PHE 0.023 0.001 PHE L 177 TRP 0.016 0.001 TRP B 86 HIS 0.008 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00280 (40049) covalent geometry : angle 0.50970 (54124) hydrogen bonds : bond 0.03631 ( 1668) hydrogen bonds : angle 4.14809 ( 4749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 330 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.8003 (tp30) cc_final: 0.7719 (mt-10) REVERT: A 1872 TYR cc_start: 0.7573 (m-80) cc_final: 0.7018 (m-10) REVERT: C 473 ASP cc_start: 0.8848 (m-30) cc_final: 0.8564 (m-30) REVERT: F 64 ASP cc_start: 0.7973 (t0) cc_final: 0.7683 (t0) REVERT: S 317 LYS cc_start: 0.8795 (tppt) cc_final: 0.8565 (pttm) REVERT: B 101 HIS cc_start: 0.7895 (m-70) cc_final: 0.7558 (m90) REVERT: B 132 MET cc_start: 0.7919 (ttp) cc_final: 0.7635 (ttp) REVERT: B 161 HIS cc_start: 0.7821 (OUTLIER) cc_final: 0.7375 (t70) REVERT: B 325 MET cc_start: -0.2421 (OUTLIER) cc_final: -0.2658 (ttp) REVERT: K 130 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7787 (mtp-110) REVERT: L 131 TYR cc_start: 0.7985 (m-80) cc_final: 0.7608 (m-80) REVERT: L 147 MET cc_start: 0.4346 (mpt) cc_final: 0.0765 (ptm) REVERT: H 112 GLU cc_start: 0.8661 (tp30) cc_final: 0.8359 (tp30) REVERT: D 184 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8570 (mmtm) REVERT: D 211 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7755 (mtm180) REVERT: E 152 LYS cc_start: 0.8173 (ptmm) cc_final: 0.7937 (ptmt) REVERT: J 130 ARG cc_start: 0.8272 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: J 168 MET cc_start: 0.7973 (ttm) cc_final: 0.7652 (ttm) REVERT: J 204 LYS cc_start: 0.8200 (tptt) cc_final: 0.7649 (tmmt) REVERT: J 248 ASP cc_start: 0.8635 (m-30) cc_final: 0.8363 (m-30) REVERT: J 288 LYS cc_start: 0.8515 (tttm) cc_final: 0.8154 (ttpm) REVERT: J 445 GLU cc_start: 0.8692 (tt0) cc_final: 0.8423 (tt0) outliers start: 78 outliers final: 32 residues processed: 383 average time/residue: 0.6671 time to fit residues: 309.1565 Evaluate side-chains 341 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 306 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 206 CYS Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 273 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 246 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 420 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 353 optimal weight: 0.3980 chunk 73 optimal weight: 1.9990 chunk 209 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN B 73 HIS B 161 HIS H 313 ASN I 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.139976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079616 restraints weight = 65055.630| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.66 r_work: 0.2913 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40049 Z= 0.111 Angle : 0.495 8.237 54124 Z= 0.258 Chirality : 0.042 0.177 6157 Planarity : 0.004 0.067 6985 Dihedral : 4.666 68.223 5488 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.27 % Favored : 96.47 % Rotamer: Outliers : 1.86 % Allowed : 11.53 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.06 (0.12), residues: 4983 helix: 1.61 (0.11), residues: 2154 sheet: 0.25 (0.18), residues: 741 loop : 0.02 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1749 TYR 0.023 0.001 TYR F 246 PHE 0.013 0.001 PHE F 47 TRP 0.011 0.001 TRP B 86 HIS 0.012 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00259 (40049) covalent geometry : angle 0.49497 (54124) hydrogen bonds : bond 0.03337 ( 1668) hydrogen bonds : angle 4.02544 ( 4749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 324 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.7999 (tp30) cc_final: 0.7723 (mt-10) REVERT: A 1872 TYR cc_start: 0.7448 (m-80) cc_final: 0.6759 (m-10) REVERT: C 473 ASP cc_start: 0.8845 (m-30) cc_final: 0.8568 (m-30) REVERT: F 64 ASP cc_start: 0.7981 (t0) cc_final: 0.7692 (t0) REVERT: S 303 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7319 (m-30) REVERT: S 317 LYS cc_start: 0.8835 (tppt) cc_final: 0.8580 (pttm) REVERT: B 44 MET cc_start: -0.6334 (ptt) cc_final: -0.8287 (mtm) REVERT: B 101 HIS cc_start: 0.7853 (m-70) cc_final: 0.7526 (m90) REVERT: B 132 MET cc_start: 0.8019 (ttp) cc_final: 0.7764 (ttp) REVERT: B 325 MET cc_start: -0.2417 (OUTLIER) cc_final: -0.2661 (ttp) REVERT: G 225 GLN cc_start: 0.7968 (tp40) cc_final: 0.7719 (tp40) REVERT: L 131 TYR cc_start: 0.8001 (m-80) cc_final: 0.7687 (m-80) REVERT: L 147 MET cc_start: 0.4336 (mpt) cc_final: 0.0857 (ptm) REVERT: L 342 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8159 (pp20) REVERT: D 184 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8578 (mmtm) REVERT: D 246 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: E 181 GLN cc_start: 0.9180 (mt0) cc_final: 0.8911 (mt0) REVERT: J 168 MET cc_start: 0.7953 (ttm) cc_final: 0.7659 (ttm) REVERT: J 204 LYS cc_start: 0.8172 (tptt) cc_final: 0.7628 (tmmt) REVERT: J 248 ASP cc_start: 0.8541 (m-30) cc_final: 0.8244 (m-30) REVERT: J 288 LYS cc_start: 0.8483 (tttm) cc_final: 0.8118 (ttpm) outliers start: 79 outliers final: 31 residues processed: 377 average time/residue: 0.6815 time to fit residues: 309.9264 Evaluate side-chains 349 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 313 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 303 ASP Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 463 optimal weight: 2.9990 chunk 86 optimal weight: 0.0050 chunk 209 optimal weight: 1.9990 chunk 431 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 366 optimal weight: 0.0980 chunk 282 optimal weight: 2.9990 chunk 257 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 231 optimal weight: 0.8980 chunk 408 optimal weight: 7.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 GLN F 102 ASN ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 ASN I 42 GLN D 226 GLN E 20 HIS E 393 HIS E 420 ASN E 450 GLN ** J 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.138837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078259 restraints weight = 64772.439| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.99 r_work: 0.2860 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40049 Z= 0.145 Angle : 0.513 8.621 54124 Z= 0.265 Chirality : 0.043 0.194 6157 Planarity : 0.004 0.059 6985 Dihedral : 4.664 66.072 5488 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.53 % Favored : 96.21 % Rotamer: Outliers : 2.33 % Allowed : 11.58 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.06 (0.12), residues: 4983 helix: 1.63 (0.11), residues: 2156 sheet: 0.34 (0.19), residues: 734 loop : -0.04 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1749 TYR 0.017 0.001 TYR A1320 PHE 0.021 0.001 PHE L 177 TRP 0.010 0.001 TRP K 394 HIS 0.009 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00349 (40049) covalent geometry : angle 0.51259 (54124) hydrogen bonds : bond 0.03568 ( 1668) hydrogen bonds : angle 4.02763 ( 4749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 321 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 1872 TYR cc_start: 0.7320 (m-80) cc_final: 0.6850 (m-10) REVERT: C 406 ARG cc_start: 0.8107 (ttt180) cc_final: 0.7686 (tmm-80) REVERT: C 473 ASP cc_start: 0.8866 (m-30) cc_final: 0.8587 (m-30) REVERT: F 64 ASP cc_start: 0.7985 (t0) cc_final: 0.7691 (t0) REVERT: F 194 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7778 (ptp90) REVERT: S 303 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: S 317 LYS cc_start: 0.8903 (tppt) cc_final: 0.8614 (pttm) REVERT: S 318 ILE cc_start: 0.9316 (mm) cc_final: 0.8974 (mm) REVERT: S 325 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8615 (mmpt) REVERT: B 47 MET cc_start: -0.2193 (OUTLIER) cc_final: -0.2524 (pp-130) REVERT: B 101 HIS cc_start: 0.7889 (m-70) cc_final: 0.7583 (m90) REVERT: B 132 MET cc_start: 0.8115 (ttp) cc_final: 0.7753 (ttp) REVERT: B 134 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 153 MET cc_start: 0.8863 (pmm) cc_final: 0.8407 (tpt) REVERT: B 173 HIS cc_start: 0.9335 (p90) cc_final: 0.8763 (p-80) REVERT: B 325 MET cc_start: -0.2171 (OUTLIER) cc_final: -0.2395 (ttp) REVERT: G 225 GLN cc_start: 0.8013 (tp40) cc_final: 0.7764 (tp40) REVERT: K 315 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7428 (mppt) REVERT: L 240 LEU cc_start: 0.4147 (OUTLIER) cc_final: 0.3879 (pt) REVERT: L 342 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8192 (pp20) REVERT: D 246 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: E 161 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7830 (mm) REVERT: E 178 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: E 181 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8960 (mt0) REVERT: J 168 MET cc_start: 0.7940 (ttm) cc_final: 0.7650 (ttm) REVERT: J 204 LYS cc_start: 0.8130 (tptt) cc_final: 0.7721 (tmmt) REVERT: J 248 ASP cc_start: 0.8537 (m-30) cc_final: 0.8258 (m-30) REVERT: J 288 LYS cc_start: 0.8484 (tttm) cc_final: 0.8084 (ttpm) outliers start: 99 outliers final: 40 residues processed: 387 average time/residue: 0.7267 time to fit residues: 340.5508 Evaluate side-chains 362 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1858 MET Chi-restraints excluded: chain A residue 2222 THR Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 303 ASP Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 12 ASN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 358 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 206 CYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 400 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 294 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 412 optimal weight: 0.8980 chunk 321 optimal weight: 0.5980 chunk 206 optimal weight: 1.9990 chunk 306 optimal weight: 0.9980 chunk 492 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 ASN H 313 ASN ** J 453 ASN ** 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 = 0.4030 r_free = 0.4030 target = 0.138981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.078538 restraints weight = 65101.096| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.99 r_work: 0.2870 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40049 Z= 0.128 Angle : 0.507 8.959 54124 Z= 0.261 Chirality : 0.042 0.187 6157 Planarity : 0.004 0.065 6985 Dihedral : 4.587 64.472 5488 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.51 % Favored : 96.19 % Rotamer: Outliers : 2.17 % Allowed : 12.07 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.11 (0.12), residues: 4983 helix: 1.68 (0.11), residues: 2157 sheet: 0.38 (0.19), residues: 730 loop : -0.04 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1749 TYR 0.024 0.001 TYR F 246 PHE 0.013 0.001 PHE F 47 TRP 0.010 0.001 TRP K 410 HIS 0.012 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00306 (40049) covalent geometry : angle 0.50688 (54124) hydrogen bonds : bond 0.03360 ( 1668) hydrogen bonds : angle 3.97000 ( 4749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 321 time to evaluate : 1.543 Fit side-chains revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7763 (mt-10) REVERT: A 1872 TYR cc_start: 0.7453 (m-80) cc_final: 0.6767 (m-10) REVERT: A 2040 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6689 (tp) REVERT: C 406 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7726 (tmm-80) REVERT: C 473 ASP cc_start: 0.8880 (m-30) cc_final: 0.8603 (m-30) REVERT: F 64 ASP cc_start: 0.7983 (t0) cc_final: 0.7679 (t0) REVERT: F 194 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7761 (ptp90) REVERT: S 297 ARG cc_start: 0.8548 (mtm-85) cc_final: 0.8280 (mtm-85) REVERT: S 303 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: S 317 LYS cc_start: 0.8930 (tppt) cc_final: 0.8642 (pttm) REVERT: S 318 ILE cc_start: 0.9300 (mm) cc_final: 0.9017 (mm) REVERT: S 325 LYS cc_start: 0.8959 (mmtm) cc_final: 0.8638 (mmpt) REVERT: B 47 MET cc_start: -0.1978 (ptt) cc_final: -0.2310 (pp-130) REVERT: B 73 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.7416 (t-170) REVERT: B 101 HIS cc_start: 0.7915 (m-70) cc_final: 0.7632 (m90) REVERT: B 132 MET cc_start: 0.8130 (ttp) cc_final: 0.7760 (ttp) REVERT: B 134 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.7884 (p) REVERT: B 153 MET cc_start: 0.8889 (pmm) cc_final: 0.8462 (tpt) REVERT: B 325 MET cc_start: -0.2050 (OUTLIER) cc_final: -0.2266 (ttp) REVERT: G 16 MET cc_start: 0.8815 (mmp) cc_final: 0.8404 (mmm) REVERT: G 225 GLN cc_start: 0.8033 (tp40) cc_final: 0.7786 (tp40) REVERT: K 315 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7336 (mppt) REVERT: L 240 LEU cc_start: 0.4275 (OUTLIER) cc_final: 0.4012 (pt) REVERT: L 342 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8190 (pp20) REVERT: D 246 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: E 178 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: E 181 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8954 (mt0) REVERT: J 130 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: J 168 MET cc_start: 0.7942 (ttm) cc_final: 0.7655 (ttm) REVERT: J 204 LYS cc_start: 0.8121 (tptt) cc_final: 0.7732 (tmmt) REVERT: J 248 ASP cc_start: 0.8538 (m-30) cc_final: 0.8252 (m-30) REVERT: J 288 LYS cc_start: 0.8510 (tttm) cc_final: 0.8126 (ttpm) outliers start: 92 outliers final: 47 residues processed: 382 average time/residue: 0.6912 time to fit residues: 318.9718 Evaluate side-chains 366 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 306 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1858 MET Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2040 ILE Chi-restraints excluded: chain A residue 2222 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 303 ASP Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 241 GLU Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 260 MET Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 358 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 349 ASP Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 178 GLU Chi-restraints excluded: chain E residue 181 GLN Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 428 optimal weight: 0.9990 chunk 242 optimal weight: 0.9990 chunk 327 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 465 optimal weight: 10.0000 chunk 198 optimal weight: 0.0670 chunk 23 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 162 optimal weight: 7.9990 chunk 363 optimal weight: 0.9990 overall best weight: 0.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1935 ASN ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN ** J 453 ASN ** 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 = 0.4038 r_free = 0.4038 target = 0.139695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078771 restraints weight = 65361.906| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.71 r_work: 0.2896 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 40049 Z= 0.111 Angle : 0.501 9.241 54124 Z= 0.258 Chirality : 0.041 0.188 6157 Planarity : 0.004 0.056 6985 Dihedral : 4.446 62.622 5487 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.43 % Favored : 96.27 % Rotamer: Outliers : 2.10 % Allowed : 12.50 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.17 (0.12), residues: 4983 helix: 1.74 (0.11), residues: 2155 sheet: 0.48 (0.19), residues: 721 loop : -0.03 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 130 TYR 0.030 0.001 TYR F 246 PHE 0.018 0.001 PHE L 177 TRP 0.010 0.001 TRP A 821 HIS 0.012 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00261 (40049) covalent geometry : angle 0.50135 (54124) hydrogen bonds : bond 0.03155 ( 1668) hydrogen bonds : angle 3.90230 ( 4749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 312 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: A 1872 TYR cc_start: 0.7415 (m-80) cc_final: 0.6709 (m-10) REVERT: A 2040 ILE cc_start: 0.6903 (OUTLIER) cc_final: 0.6549 (pp) REVERT: C 406 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7781 (tmm-80) REVERT: C 473 ASP cc_start: 0.8853 (m-30) cc_final: 0.8578 (m-30) REVERT: F 64 ASP cc_start: 0.8030 (t0) cc_final: 0.7720 (t0) REVERT: F 194 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7756 (ptp90) REVERT: S 303 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: S 310 TYR cc_start: 0.8626 (p90) cc_final: 0.8137 (p90) REVERT: S 317 LYS cc_start: 0.8936 (tppt) cc_final: 0.8623 (pttm) REVERT: S 318 ILE cc_start: 0.9293 (mm) cc_final: 0.9001 (mm) REVERT: S 325 LYS cc_start: 0.8992 (mmtm) cc_final: 0.8646 (mmpt) REVERT: B 73 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7403 (t-170) REVERT: B 101 HIS cc_start: 0.7899 (m-70) cc_final: 0.7611 (m90) REVERT: B 132 MET cc_start: 0.8152 (ttp) cc_final: 0.7746 (ttp) REVERT: B 134 VAL cc_start: 0.8396 (OUTLIER) cc_final: 0.7889 (p) REVERT: B 153 MET cc_start: 0.8860 (pmm) cc_final: 0.8454 (tpt) REVERT: B 173 HIS cc_start: 0.9341 (p90) cc_final: 0.8785 (p-80) REVERT: B 325 MET cc_start: -0.2131 (OUTLIER) cc_final: -0.2392 (ttp) REVERT: G 225 GLN cc_start: 0.8061 (tp40) cc_final: 0.7805 (tp40) REVERT: K 315 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7210 (mppt) REVERT: L 240 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.4110 (pt) REVERT: L 323 ILE cc_start: 0.8540 (pt) cc_final: 0.8260 (mt) REVERT: L 342 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: D 246 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8285 (mt-10) REVERT: J 130 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7992 (mtm-85) REVERT: J 204 LYS cc_start: 0.8116 (tptt) cc_final: 0.7702 (tmmt) REVERT: J 248 ASP cc_start: 0.8576 (m-30) cc_final: 0.8308 (m-30) REVERT: J 288 LYS cc_start: 0.8530 (tttm) cc_final: 0.8123 (ttpm) outliers start: 89 outliers final: 41 residues processed: 371 average time/residue: 0.6680 time to fit residues: 299.9484 Evaluate side-chains 359 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 307 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 2040 ILE Chi-restraints excluded: chain A residue 2222 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 300 LEU Chi-restraints excluded: chain S residue 303 ASP Chi-restraints excluded: chain S residue 306 THR Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 358 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 229 optimal weight: 0.6980 chunk 333 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 chunk 490 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 371 optimal weight: 3.9990 chunk 475 optimal weight: 5.9990 chunk 113 optimal weight: 0.8980 chunk 54 optimal weight: 0.0270 chunk 95 optimal weight: 0.7980 chunk 204 optimal weight: 0.8980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 313 ASN I 42 GLN ** J 453 ASN ** 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 = 0.4037 r_free = 0.4037 target = 0.139621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078725 restraints weight = 65483.870| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.70 r_work: 0.2895 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40049 Z= 0.114 Angle : 0.509 10.445 54124 Z= 0.261 Chirality : 0.041 0.177 6157 Planarity : 0.004 0.056 6985 Dihedral : 4.411 61.291 5487 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.41 % Favored : 96.31 % Rotamer: Outliers : 1.77 % Allowed : 12.69 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.22 (0.12), residues: 4983 helix: 1.77 (0.11), residues: 2150 sheet: 0.48 (0.19), residues: 721 loop : 0.00 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 210 TYR 0.029 0.001 TYR F 246 PHE 0.017 0.001 PHE E 177 TRP 0.010 0.001 TRP S 277 HIS 0.015 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00269 (40049) covalent geometry : angle 0.50912 (54124) hydrogen bonds : bond 0.03152 ( 1668) hydrogen bonds : angle 3.88665 ( 4749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 312 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7776 (mt-10) REVERT: A 1872 TYR cc_start: 0.7447 (m-80) cc_final: 0.6703 (m-10) REVERT: A 2040 ILE cc_start: 0.6852 (OUTLIER) cc_final: 0.6516 (pp) REVERT: C 406 ARG cc_start: 0.8184 (ttt180) cc_final: 0.7795 (tmm-80) REVERT: C 473 ASP cc_start: 0.8830 (m-30) cc_final: 0.8558 (m-30) REVERT: F 64 ASP cc_start: 0.8050 (t0) cc_final: 0.7722 (t0) REVERT: F 194 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7760 (ptp90) REVERT: S 297 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8363 (mtm-85) REVERT: S 303 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: S 310 TYR cc_start: 0.8629 (p90) cc_final: 0.8209 (p90) REVERT: S 317 LYS cc_start: 0.8948 (tppt) cc_final: 0.8643 (pttm) REVERT: S 318 ILE cc_start: 0.9294 (mm) cc_final: 0.9005 (mm) REVERT: S 325 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8663 (mmpt) REVERT: B 73 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.7514 (t-170) REVERT: B 101 HIS cc_start: 0.7886 (m-70) cc_final: 0.7616 (m90) REVERT: B 132 MET cc_start: 0.8170 (ttp) cc_final: 0.7760 (ttp) REVERT: B 134 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.7856 (p) REVERT: B 153 MET cc_start: 0.8921 (pmm) cc_final: 0.8517 (tpt) REVERT: B 325 MET cc_start: -0.2032 (OUTLIER) cc_final: -0.2268 (ttp) REVERT: G 225 GLN cc_start: 0.8077 (tp40) cc_final: 0.7815 (tp40) REVERT: K 315 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7128 (mppt) REVERT: L 240 LEU cc_start: 0.4375 (OUTLIER) cc_final: 0.4119 (pt) REVERT: L 323 ILE cc_start: 0.8514 (pt) cc_final: 0.8234 (mt) REVERT: L 342 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8205 (tm-30) REVERT: D 246 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: E 161 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7822 (mm) REVERT: E 178 GLU cc_start: 0.8194 (pt0) cc_final: 0.7948 (tm-30) REVERT: E 181 GLN cc_start: 0.9293 (tt0) cc_final: 0.9061 (tt0) REVERT: E 206 CYS cc_start: 0.8364 (m) cc_final: 0.8108 (p) REVERT: J 130 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7999 (mtm-85) REVERT: J 201 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8106 (mmmm) REVERT: J 204 LYS cc_start: 0.8113 (tptt) cc_final: 0.7690 (tmmt) REVERT: J 237 GLU cc_start: 0.7475 (tp30) cc_final: 0.7066 (tp30) REVERT: J 248 ASP cc_start: 0.8545 (m-30) cc_final: 0.8278 (m-30) REVERT: J 288 LYS cc_start: 0.8531 (tttm) cc_final: 0.8133 (ttpm) outliers start: 75 outliers final: 41 residues processed: 363 average time/residue: 0.7015 time to fit residues: 308.8032 Evaluate side-chains 363 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 2040 ILE Chi-restraints excluded: chain A residue 2222 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 303 ASP Chi-restraints excluded: chain S residue 306 THR Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 358 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 146 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 473 optimal weight: 20.0000 chunk 445 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 178 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 378 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 264 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2034 ASN H 313 ASN ** J 453 ASN ** 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 = 0.4029 r_free = 0.4029 target = 0.138936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.077868 restraints weight = 65423.811| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.71 r_work: 0.2879 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40049 Z= 0.135 Angle : 0.521 10.262 54124 Z= 0.266 Chirality : 0.042 0.192 6157 Planarity : 0.004 0.057 6985 Dihedral : 4.439 59.973 5487 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.61 % Favored : 96.11 % Rotamer: Outliers : 1.74 % Allowed : 12.78 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.18 (0.12), residues: 4983 helix: 1.74 (0.11), residues: 2153 sheet: 0.45 (0.19), residues: 723 loop : -0.01 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 130 TYR 0.032 0.001 TYR F 246 PHE 0.016 0.001 PHE E 177 TRP 0.011 0.001 TRP S 277 HIS 0.014 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00323 (40049) covalent geometry : angle 0.52084 (54124) hydrogen bonds : bond 0.03339 ( 1668) hydrogen bonds : angle 3.92893 ( 4749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 314 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: A 1872 TYR cc_start: 0.7468 (m-80) cc_final: 0.6701 (m-10) REVERT: A 2040 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6525 (pp) REVERT: C 406 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7795 (tmm-80) REVERT: C 473 ASP cc_start: 0.8839 (m-30) cc_final: 0.8568 (m-30) REVERT: F 64 ASP cc_start: 0.8055 (t0) cc_final: 0.7741 (t0) REVERT: F 194 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7781 (ptp90) REVERT: S 297 ARG cc_start: 0.8642 (mtm-85) cc_final: 0.8289 (mtm-85) REVERT: S 303 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7459 (m-30) REVERT: S 310 TYR cc_start: 0.8680 (p90) cc_final: 0.8246 (p90) REVERT: S 317 LYS cc_start: 0.8954 (tppt) cc_final: 0.8688 (pttm) REVERT: S 325 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8623 (mmpt) REVERT: B 47 MET cc_start: -0.1560 (pp-130) cc_final: -0.2022 (pp-130) REVERT: B 73 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.7498 (t-170) REVERT: B 101 HIS cc_start: 0.7888 (m-70) cc_final: 0.7618 (m90) REVERT: B 132 MET cc_start: 0.8133 (ttp) cc_final: 0.7757 (ttp) REVERT: B 134 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.7961 (p) REVERT: B 153 MET cc_start: 0.8926 (pmm) cc_final: 0.8571 (tpt) REVERT: B 227 MET cc_start: 0.5923 (tpp) cc_final: 0.5195 (mmp) REVERT: B 325 MET cc_start: -0.1970 (OUTLIER) cc_final: -0.2209 (ttp) REVERT: G 225 GLN cc_start: 0.8091 (tp40) cc_final: 0.7829 (tp40) REVERT: K 315 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7099 (mppt) REVERT: L 240 LEU cc_start: 0.4436 (OUTLIER) cc_final: 0.4086 (pt) REVERT: L 264 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7914 (mtt) REVERT: L 342 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: D 246 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8313 (mt-10) REVERT: E 161 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7776 (mm) REVERT: E 178 GLU cc_start: 0.8252 (pt0) cc_final: 0.8034 (pp20) REVERT: J 130 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8020 (mtm-85) REVERT: J 201 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8086 (mmmm) REVERT: J 204 LYS cc_start: 0.8110 (tptt) cc_final: 0.7725 (tmmt) REVERT: J 237 GLU cc_start: 0.7489 (tp30) cc_final: 0.7078 (tp30) REVERT: J 288 LYS cc_start: 0.8525 (tttm) cc_final: 0.8110 (ttpm) outliers start: 74 outliers final: 43 residues processed: 361 average time/residue: 0.7066 time to fit residues: 309.0873 Evaluate side-chains 365 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2040 ILE Chi-restraints excluded: chain A residue 2222 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 303 ASP Chi-restraints excluded: chain S residue 306 THR Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain L residue 343 ASP Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain H residue 22 ILE Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 358 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 222 optimal weight: 1.9990 chunk 282 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 336 optimal weight: 20.0000 chunk 198 optimal weight: 5.9990 chunk 443 optimal weight: 0.7980 chunk 191 optimal weight: 0.5980 chunk 123 optimal weight: 9.9990 chunk 23 optimal weight: 0.0770 chunk 260 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 313 ASN E 181 GLN E 241 HIS ** J 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.139348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079094 restraints weight = 65219.283| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.66 r_work: 0.2897 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 40049 Z= 0.112 Angle : 0.513 9.990 54124 Z= 0.262 Chirality : 0.041 0.178 6157 Planarity : 0.004 0.061 6985 Dihedral : 4.376 58.128 5487 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.35 % Favored : 96.37 % Rotamer: Outliers : 1.58 % Allowed : 12.95 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.23 (0.12), residues: 4983 helix: 1.78 (0.11), residues: 2157 sheet: 0.49 (0.19), residues: 723 loop : 0.00 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 130 TYR 0.032 0.001 TYR F 246 PHE 0.010 0.001 PHE K 37 TRP 0.010 0.001 TRP F 114 HIS 0.015 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00262 (40049) covalent geometry : angle 0.51314 (54124) hydrogen bonds : bond 0.03098 ( 1668) hydrogen bonds : angle 3.86830 ( 4749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9966 Ramachandran restraints generated. 4983 Oldfield, 0 Emsley, 4983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 322 time to evaluate : 1.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1389 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7789 (mt-10) REVERT: A 1872 TYR cc_start: 0.7485 (m-80) cc_final: 0.6703 (m-10) REVERT: A 2040 ILE cc_start: 0.6881 (OUTLIER) cc_final: 0.6547 (pp) REVERT: C 406 ARG cc_start: 0.8178 (ttt180) cc_final: 0.7782 (tmm-80) REVERT: C 473 ASP cc_start: 0.8830 (m-30) cc_final: 0.8564 (m-30) REVERT: F 64 ASP cc_start: 0.8026 (t0) cc_final: 0.7713 (t0) REVERT: F 194 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7755 (ptp90) REVERT: S 297 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8353 (mtm-85) REVERT: S 303 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: S 310 TYR cc_start: 0.8700 (p90) cc_final: 0.8409 (p90) REVERT: S 317 LYS cc_start: 0.8960 (tppt) cc_final: 0.8674 (pttm) REVERT: S 318 ILE cc_start: 0.9303 (mt) cc_final: 0.8975 (mp) REVERT: S 325 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8610 (mmpt) REVERT: B 73 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7558 (t-170) REVERT: B 101 HIS cc_start: 0.7881 (m-70) cc_final: 0.7612 (m90) REVERT: B 132 MET cc_start: 0.8064 (ttp) cc_final: 0.7588 (ttp) REVERT: B 153 MET cc_start: 0.8920 (pmm) cc_final: 0.8602 (tpt) REVERT: B 325 MET cc_start: -0.1967 (OUTLIER) cc_final: -0.2208 (ttp) REVERT: G 225 GLN cc_start: 0.8088 (tp40) cc_final: 0.7827 (tp40) REVERT: K 315 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7084 (mppt) REVERT: L 147 MET cc_start: 0.4223 (mpt) cc_final: 0.0415 (ptm) REVERT: L 240 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.4035 (pt) REVERT: L 264 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7926 (mtt) REVERT: L 323 ILE cc_start: 0.8485 (pt) cc_final: 0.8230 (mt) REVERT: L 342 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: D 246 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: E 161 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7774 (mm) REVERT: E 178 GLU cc_start: 0.8239 (pt0) cc_final: 0.8014 (pp20) REVERT: E 206 CYS cc_start: 0.8345 (m) cc_final: 0.8138 (p) REVERT: E 308 ASP cc_start: 0.8028 (m-30) cc_final: 0.7740 (m-30) REVERT: J 130 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8025 (mtm-85) REVERT: J 204 LYS cc_start: 0.8129 (tptt) cc_final: 0.7713 (tmmt) REVERT: J 237 GLU cc_start: 0.7477 (tp30) cc_final: 0.7061 (tp30) REVERT: J 248 ASP cc_start: 0.8538 (m-30) cc_final: 0.8254 (m-30) REVERT: J 288 LYS cc_start: 0.8522 (tttm) cc_final: 0.8115 (ttpm) outliers start: 67 outliers final: 42 residues processed: 365 average time/residue: 0.6979 time to fit residues: 308.0780 Evaluate side-chains 364 residues out of total 4309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 310 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 833 LYS Chi-restraints excluded: chain A residue 1227 MET Chi-restraints excluded: chain A residue 1389 GLU Chi-restraints excluded: chain A residue 1858 MET Chi-restraints excluded: chain A residue 2032 LEU Chi-restraints excluded: chain A residue 2040 ILE Chi-restraints excluded: chain A residue 2222 THR Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain F residue 194 ARG Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 231 GLU Chi-restraints excluded: chain S residue 273 THR Chi-restraints excluded: chain S residue 288 VAL Chi-restraints excluded: chain S residue 303 ASP Chi-restraints excluded: chain S residue 349 LEU Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 315 LYS Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 139 THR Chi-restraints excluded: chain L residue 240 LEU Chi-restraints excluded: chain L residue 264 MET Chi-restraints excluded: chain L residue 308 ASP Chi-restraints excluded: chain L residue 342 GLU Chi-restraints excluded: chain L residue 407 VAL Chi-restraints excluded: chain H residue 170 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 306 ILE Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 358 VAL Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 445 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 193 ILE Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain J residue 17 THR Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 301 VAL Chi-restraints excluded: chain J residue 305 ASP Chi-restraints excluded: chain J residue 349 ASP Chi-restraints excluded: chain J residue 357 VAL Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 421 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 426 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 119 optimal weight: 0.1980 chunk 404 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 482 optimal weight: 0.8980 chunk 224 optimal weight: 0.7980 chunk 297 optimal weight: 3.9990 chunk 245 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 313 ASN I 42 GLN D 313 ASN ** J 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.139908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.078938 restraints weight = 65504.714| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.73 r_work: 0.2898 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 40049 Z= 0.106 Angle : 0.510 11.027 54124 Z= 0.260 Chirality : 0.041 0.179 6157 Planarity : 0.004 0.060 6985 Dihedral : 4.264 56.906 5485 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.55 % Favored : 96.19 % Rotamer: Outliers : 1.44 % Allowed : 13.20 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.28 (0.12), residues: 4983 helix: 1.82 (0.11), residues: 2150 sheet: 0.53 (0.19), residues: 713 loop : 0.03 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 130 TYR 0.020 0.001 TYR E 192 PHE 0.013 0.001 PHE L 177 TRP 0.014 0.001 TRP S 277 HIS 0.015 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00248 (40049) covalent geometry : angle 0.51005 (54124) hydrogen bonds : bond 0.03045 ( 1668) hydrogen bonds : angle 3.84058 ( 4749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21969.43 seconds wall clock time: 371 minutes 51.94 seconds (22311.94 seconds total)