Starting phenix.real_space_refine on Tue Aug 26 19:15:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvt_38718/08_2025/8xvt_38718.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvt_38718/08_2025/8xvt_38718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xvt_38718/08_2025/8xvt_38718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvt_38718/08_2025/8xvt_38718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xvt_38718/08_2025/8xvt_38718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvt_38718/08_2025/8xvt_38718.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1351 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 204 5.16 5 C 24551 2.51 5 N 6829 2.21 5 O 7385 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38987 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3279 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 16, 'TRANS': 409} Chain breaks: 1 Chain: "B" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3101 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 11, 'TRANS': 387} Chain breaks: 3 Chain: "C" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3210 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 16, 'TRANS': 399} Chain breaks: 2 Chain: "D" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3315 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 1 Chain: "E" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3344 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 17, 'TRANS': 417} Chain: "F" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3242 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 9, 'TRANS': 407} Chain breaks: 2 Chain: "G" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1717 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain breaks: 1 Chain: "H" Number of atoms: 6900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6900 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 39, 'TRANS': 801} Chain breaks: 5 Chain: "I" Number of atoms: 2715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2715 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 15, 'TRANS': 333} Chain breaks: 3 Chain: "J" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3139 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 20, 'TRANS': 382} Chain breaks: 1 Chain: "K" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2733 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 18, 'TRANS': 331} Chain breaks: 1 Chain: "M" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 861 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Chain: "N" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1188 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 23, 'TRANS': 126} Chain breaks: 2 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.27, per 1000 atoms: 0.19 Number of scatterers: 38987 At special positions: 0 Unit cell: (150.742, 214.774, 193.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 204 16.00 P 18 15.00 O 7385 8.00 N 6829 7.00 C 24551 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=11, symmetry=0 Number of additional bonds: simple=11, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.21 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 953.7 nanoseconds 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9170 Finding SS restraints... Secondary structure from input PDB file: 217 helices and 48 sheets defined 46.6% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.609A pdb=" N GLU A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 99 through 102 Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 173 through 183 removed outlier: 3.525A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 275 through 289 Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 319 removed outlier: 3.854A pdb=" N TYR A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 383 Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.506A pdb=" N THR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 421 removed outlier: 3.765A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 411 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Proline residue: A 412 - end of helix Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.699A pdb=" N ALA A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 4.357A pdb=" N HIS B 27 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 66 Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.661A pdb=" N ALA B 87 " --> pdb=" O LYS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 125 Processing helix chain 'B' and resid 175 through 180 removed outlier: 4.049A pdb=" N GLU B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 250 Processing helix chain 'B' and resid 255 through 260 Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.564A pdb=" N ILE B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 305 through 316 removed outlier: 3.860A pdb=" N ARG B 314 " --> pdb=" O SER B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 363 through 378 Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 398 through 416 Processing helix chain 'B' and resid 422 through 433 Processing helix chain 'B' and resid 435 through 442 Processing helix chain 'B' and resid 443 through 446 Processing helix chain 'C' and resid 42 through 59 Processing helix chain 'C' and resid 75 through 88 Processing helix chain 'C' and resid 99 through 102 Processing helix chain 'C' and resid 107 through 120 removed outlier: 3.688A pdb=" N ILE C 120 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 240 through 249 Processing helix chain 'C' and resid 255 through 262 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.908A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 Processing helix chain 'C' and resid 351 through 358 removed outlier: 3.651A pdb=" N ARG C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 383 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 421 removed outlier: 4.461A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix Processing helix chain 'C' and resid 426 through 437 Processing helix chain 'C' and resid 439 through 446 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.572A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.589A pdb=" N SER D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 247 through 252 removed outlier: 4.370A pdb=" N SER D 252 " --> pdb=" O ASP D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 261 Processing helix chain 'D' and resid 272 through 287 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.522A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 354 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 417 Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.521A pdb=" N SER D 431 " --> pdb=" O LYS D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 443 Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'E' and resid 42 through 59 Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 99 through 102 Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.529A pdb=" N ARG E 249 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 276 Processing helix chain 'E' and resid 277 through 289 Processing helix chain 'E' and resid 304 through 307 Processing helix chain 'E' and resid 308 through 319 removed outlier: 3.798A pdb=" N TYR E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 350 Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.584A pdb=" N ASP E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 383 Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 402 through 409 removed outlier: 4.206A pdb=" N SER E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 407 " --> pdb=" O LEU E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 421 Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'F' and resid 105 through 109 removed outlier: 4.060A pdb=" N PHE F 109 " --> pdb=" O GLY F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 109' Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 245 through 249 Processing helix chain 'F' and resid 268 through 274 Processing helix chain 'F' and resid 275 through 286 Processing helix chain 'F' and resid 301 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.780A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 417 removed outlier: 3.733A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.547A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 Processing helix chain 'F' and resid 443 through 446 Processing helix chain 'G' and resid 83 through 89 Processing helix chain 'G' and resid 102 through 106 removed outlier: 3.718A pdb=" N LYS G 106 " --> pdb=" O PRO G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 120 No H-bonds generated for 'chain 'G' and resid 118 through 120' Processing helix chain 'G' and resid 124 through 130 removed outlier: 3.674A pdb=" N ALA G 127 " --> pdb=" O TYR G 124 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG G 128 " --> pdb=" O PRO G 125 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN G 130 " --> pdb=" O ALA G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 153 through 168 Processing helix chain 'G' and resid 170 through 178 Processing helix chain 'G' and resid 187 through 207 Processing helix chain 'G' and resid 229 through 245 removed outlier: 3.756A pdb=" N LEU G 233 " --> pdb=" O GLN G 229 " (cutoff:3.500A) Proline residue: G 238 - end of helix Processing helix chain 'G' and resid 247 through 275 Processing helix chain 'H' and resid 740 through 751 Processing helix chain 'H' and resid 774 through 858 removed outlier: 3.652A pdb=" N GLU H 781 " --> pdb=" O ASP H 777 " (cutoff:3.500A) Processing helix chain 'H' and resid 1056 through 1066 Processing helix chain 'H' and resid 1066 through 1073 removed outlier: 4.279A pdb=" N TYR H1070 " --> pdb=" O LEU H1066 " (cutoff:3.500A) Processing helix chain 'H' and resid 1085 through 1101 removed outlier: 3.640A pdb=" N ALA H1098 " --> pdb=" O PHE H1094 " (cutoff:3.500A) Processing helix chain 'H' and resid 1112 through 1114 No H-bonds generated for 'chain 'H' and resid 1112 through 1114' Processing helix chain 'H' and resid 1115 through 1126 Processing helix chain 'H' and resid 1140 through 1146 removed outlier: 3.532A pdb=" N ALA H1144 " --> pdb=" O ARG H1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 1162 through 1166 removed outlier: 3.915A pdb=" N PHE H1166 " --> pdb=" O TYR H1162 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1162 through 1166' Processing helix chain 'H' and resid 1168 through 1173 Processing helix chain 'H' and resid 1185 through 1189 removed outlier: 3.714A pdb=" N LYS H1189 " --> pdb=" O GLN H1186 " (cutoff:3.500A) Processing helix chain 'H' and resid 1194 through 1201 removed outlier: 3.947A pdb=" N THR H1201 " --> pdb=" O GLU H1197 " (cutoff:3.500A) Processing helix chain 'H' and resid 1218 through 1230 removed outlier: 4.110A pdb=" N LEU H1222 " --> pdb=" O THR H1218 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL H1230 " --> pdb=" O VAL H1226 " (cutoff:3.500A) Processing helix chain 'H' and resid 1256 through 1264 Processing helix chain 'H' and resid 1272 through 1277 removed outlier: 3.871A pdb=" N ASP H1275 " --> pdb=" O THR H1272 " (cutoff:3.500A) Processing helix chain 'H' and resid 1293 through 1305 Processing helix chain 'H' and resid 1307 through 1313 removed outlier: 3.956A pdb=" N GLU H1311 " --> pdb=" O PRO H1307 " (cutoff:3.500A) Processing helix chain 'H' and resid 1317 through 1332 Processing helix chain 'H' and resid 1334 through 1339 removed outlier: 4.060A pdb=" N VAL H1338 " --> pdb=" O HIS H1334 " (cutoff:3.500A) Processing helix chain 'H' and resid 1357 through 1362 removed outlier: 4.354A pdb=" N LEU H1361 " --> pdb=" O ALA H1357 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS H1362 " --> pdb=" O SER H1358 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1357 through 1362' Processing helix chain 'H' and resid 1377 through 1383 removed outlier: 3.793A pdb=" N ILE H1380 " --> pdb=" O PHE H1377 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY H1381 " --> pdb=" O ASP H1378 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1394 Processing helix chain 'H' and resid 1728 through 1741 Processing helix chain 'H' and resid 1742 through 1744 No H-bonds generated for 'chain 'H' and resid 1742 through 1744' Processing helix chain 'H' and resid 1750 through 1755 removed outlier: 3.758A pdb=" N ASP H1754 " --> pdb=" O ARG H1750 " (cutoff:3.500A) Processing helix chain 'H' and resid 1790 through 1798 removed outlier: 3.687A pdb=" N VAL H1798 " --> pdb=" O ARG H1794 " (cutoff:3.500A) Processing helix chain 'H' and resid 1818 through 1834 Processing helix chain 'H' and resid 1838 through 1845 removed outlier: 3.638A pdb=" N ARG H1841 " --> pdb=" O GLN H1838 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN H1842 " --> pdb=" O GLN H1839 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR H1844 " --> pdb=" O ARG H1841 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA H1845 " --> pdb=" O GLN H1842 " (cutoff:3.500A) Processing helix chain 'H' and resid 1854 through 1860 removed outlier: 4.317A pdb=" N GLN H1858 " --> pdb=" O LEU H1854 " (cutoff:3.500A) Processing helix chain 'H' and resid 1861 through 1878 Processing helix chain 'H' and resid 1887 through 1902 Processing helix chain 'H' and resid 1913 through 1925 Processing helix chain 'H' and resid 1962 through 1975 Processing helix chain 'H' and resid 1990 through 1998 removed outlier: 3.988A pdb=" N LYS H1994 " --> pdb=" O SER H1990 " (cutoff:3.500A) Processing helix chain 'H' and resid 2000 through 2005 Processing helix chain 'H' and resid 2018 through 2024 removed outlier: 4.258A pdb=" N ARG H2022 " --> pdb=" O PHE H2018 " (cutoff:3.500A) Processing helix chain 'H' and resid 2149 through 2180 Processing helix chain 'H' and resid 2188 through 2193 Processing helix chain 'H' and resid 2227 through 2232 removed outlier: 3.802A pdb=" N LEU H2232 " --> pdb=" O VAL H2229 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 77 Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 129 through 144 Processing helix chain 'I' and resid 153 through 163 removed outlier: 3.635A pdb=" N LEU I 157 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.758A pdb=" N ILE I 192 " --> pdb=" O GLN I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 212 removed outlier: 3.580A pdb=" N GLU I 208 " --> pdb=" O MET I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 267 Processing helix chain 'I' and resid 298 through 309 removed outlier: 3.763A pdb=" N ARG I 301 " --> pdb=" O GLY I 298 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE I 304 " --> pdb=" O ARG I 301 " (cutoff:3.500A) Proline residue: I 305 - end of helix Processing helix chain 'I' and resid 324 through 335 Processing helix chain 'I' and resid 340 through 346 Processing helix chain 'I' and resid 354 through 357 Processing helix chain 'I' and resid 359 through 369 Processing helix chain 'I' and resid 386 through 390 removed outlier: 3.734A pdb=" N ARG I 389 " --> pdb=" O THR I 386 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG I 390 " --> pdb=" O VAL I 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 386 through 390' Processing helix chain 'I' and resid 391 through 401 removed outlier: 3.676A pdb=" N ALA I 401 " --> pdb=" O GLY I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 409 Processing helix chain 'J' and resid 73 through 77 removed outlier: 3.756A pdb=" N VAL J 77 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 111 Processing helix chain 'J' and resid 114 through 118 removed outlier: 3.882A pdb=" N HIS J 118 " --> pdb=" O ALA J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 143 Processing helix chain 'J' and resid 154 through 162 removed outlier: 3.587A pdb=" N ASN J 162 " --> pdb=" O THR J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 192 removed outlier: 3.652A pdb=" N ILE J 192 " --> pdb=" O GLN J 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 189 through 192' Processing helix chain 'J' and resid 198 through 214 Processing helix chain 'J' and resid 247 through 266 removed outlier: 3.607A pdb=" N VAL J 258 " --> pdb=" O MET J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 282 removed outlier: 3.504A pdb=" N MET J 282 " --> pdb=" O ALA J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 removed outlier: 3.622A pdb=" N GLU J 306 " --> pdb=" O LYS J 303 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY J 307 " --> pdb=" O ILE J 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 303 through 307' Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 340 through 346 removed outlier: 3.553A pdb=" N GLY J 346 " --> pdb=" O PRO J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 353 through 357 Processing helix chain 'J' and resid 359 through 372 Processing helix chain 'J' and resid 391 through 403 Processing helix chain 'J' and resid 404 through 409 removed outlier: 3.710A pdb=" N GLN J 408 " --> pdb=" O THR J 405 " (cutoff:3.500A) Processing helix chain 'J' and resid 413 through 418 Processing helix chain 'K' and resid 78 through 92 removed outlier: 3.635A pdb=" N MET K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 101 Processing helix chain 'K' and resid 112 through 126 Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 171 through 175 Processing helix chain 'K' and resid 181 through 196 Processing helix chain 'K' and resid 202 through 216 removed outlier: 4.298A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 233 removed outlier: 4.007A pdb=" N ALA K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 237 Processing helix chain 'K' and resid 252 through 257 removed outlier: 3.731A pdb=" N ARG K 256 " --> pdb=" O ASN K 252 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS K 257 " --> pdb=" O GLU K 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 252 through 257' Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 273 through 285 Processing helix chain 'K' and resid 289 through 295 Processing helix chain 'K' and resid 301 through 305 Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 356 removed outlier: 3.745A pdb=" N GLN K 354 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 367 through 371 Processing helix chain 'M' and resid 435 through 437 No H-bonds generated for 'chain 'M' and resid 435 through 437' Processing helix chain 'M' and resid 461 through 463 No H-bonds generated for 'chain 'M' and resid 461 through 463' Processing helix chain 'M' and resid 472 through 475 Processing helix chain 'M' and resid 476 through 481 Processing helix chain 'M' and resid 481 through 486 Processing helix chain 'M' and resid 514 through 519 Processing helix chain 'N' and resid 173 through 190 Processing helix chain 'N' and resid 196 through 207 Processing helix chain 'N' and resid 270 through 278 removed outlier: 3.674A pdb=" N PHE N 274 " --> pdb=" O ASP N 270 " (cutoff:3.500A) Processing helix chain 'N' and resid 312 through 329 removed outlier: 3.844A pdb=" N ALA N 329 " --> pdb=" O LYS N 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.202A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 330 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA A 65 " --> pdb=" O MET A 359 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE A 361 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 67 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 230 through 239 removed outlier: 3.816A pdb=" N LYS A 230 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 172 removed outlier: 3.954A pdb=" N VAL A 157 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 12.185A pdb=" N HIS A 156 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 10.675A pdb=" N LEU A 138 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 10.401A pdb=" N ILE A 158 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N THR A 136 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A 160 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 191 " --> pdb=" O GLY A 133 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 337 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 104 removed outlier: 6.385A pdb=" N THR B 101 " --> pdb=" O PHE B 297 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ASP B 299 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE B 103 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 327 " --> pdb=" O ILE B 298 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 77 " --> pdb=" O THR B 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 242 removed outlier: 3.720A pdb=" N LYS B 234 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE B 137 " --> pdb=" O LYS B 234 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS B 236 " --> pdb=" O THR B 135 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 135 " --> pdb=" O LYS B 236 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 332 through 334 Processing sheet with id=AA9, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.614A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 121 through 137 removed outlier: 6.228A pdb=" N GLY C 160 " --> pdb=" O THR C 136 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 167 through 172 current: chain 'C' and resid 200 through 206 Processing sheet with id=AB3, first strand: chain 'C' and resid 336 through 337 Processing sheet with id=AB4, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 104 removed outlier: 3.527A pdb=" N ALA D 327 " --> pdb=" O ILE D 298 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 236 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 137 through 144 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 137 through 144 current: chain 'D' and resid 158 through 164 removed outlier: 4.144A 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 204 through 207 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 204 through 207 current: chain 'N' and resid 260 through 268 Processing sheet with id=AB8, first strand: chain 'D' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'E' and resid 93 through 97 removed outlier: 5.987A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 120 through 134 removed outlier: 3.889A pdb=" N GLY E 133 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE E 191 " --> pdb=" O GLY E 133 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 190 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N VAL E 221 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG E 205 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 137 through 138 removed outlier: 3.514A pdb=" N LEU E 161 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 214 through 215 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 214 through 215 current: chain 'F' and resid 160 through 164 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 174 current: chain 'F' and resid 201 through 205 Processing sheet with id=AC4, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AC5, first strand: chain 'F' and resid 100 through 104 removed outlier: 3.632A pdb=" N ALA F 327 " --> pdb=" O ILE F 298 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 332 through 334 removed outlier: 3.591A pdb=" N THR F 333 " --> pdb=" O SER F 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 61 through 62 removed outlier: 3.568A pdb=" N LEU G 61 " --> pdb=" O TYR M 440 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ARG M 439 " --> pdb=" O ARG M 457 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ARG M 457 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY M 453 " --> pdb=" O THR M 443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 95 through 100 Processing sheet with id=AC9, first strand: chain 'H' and resid 766 through 767 removed outlier: 3.972A pdb=" N ALA H2236 " --> pdb=" O ALA M 414 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 1077 through 1079 removed outlier: 6.163A pdb=" N LEU H1180 " --> pdb=" O LEU H1208 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU H1210 " --> pdb=" O LEU H1180 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE H1182 " --> pdb=" O LEU H1210 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP H1183 " --> pdb=" O VAL H1110 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU H1133 " --> pdb=" O ILE H1159 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N SER H1161 " --> pdb=" O LEU H1133 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 1283 through 1290 removed outlier: 3.597A pdb=" N VAL H1986 " --> pdb=" O LEU H1288 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU H1882 " --> pdb=" O VAL H1953 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 1353 through 1354 removed outlier: 3.545A pdb=" N TYR H1354 " --> pdb=" O VAL H1811 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'H' and resid 2198 through 2200 removed outlier: 3.756A pdb=" N TYR H2199 " --> pdb=" O GLU H2207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU H2207 " --> pdb=" O TYR H2199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'I' and resid 35 through 38 removed outlier: 3.805A pdb=" N PHE I 37 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU I 14 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N SER I 123 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE I 16 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL I 120 " --> pdb=" O PHE I 150 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N CYS I 152 " --> pdb=" O VAL I 120 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N MET I 122 " --> pdb=" O CYS I 152 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 41 through 43 Processing sheet with id=AD7, first strand: chain 'I' and resid 88 through 89 Processing sheet with id=AD8, first strand: chain 'I' and resid 177 through 182 removed outlier: 5.716A pdb=" N LEU I 168 " --> pdb=" O ILE I 349 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA I 351 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU I 170 " --> pdb=" O ALA I 351 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL I 348 " --> pdb=" O LYS I 379 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 280 through 282 removed outlier: 3.976A pdb=" N CYS I 295 " --> pdb=" O MET I 282 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 15 through 17 removed outlier: 3.507A pdb=" N PHE J 37 " --> pdb=" O VAL J 23 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AE3, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AE4, first strand: chain 'J' and resid 123 through 124 Processing sheet with id=AE5, first strand: chain 'J' and resid 148 through 149 Processing sheet with id=AE6, first strand: chain 'J' and resid 186 through 187 removed outlier: 3.538A pdb=" N GLY J 167 " --> pdb=" O VAL J 182 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N LEU J 168 " --> pdb=" O ILE J 349 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 223 through 225 removed outlier: 6.864A pdb=" N LYS J 238 " --> pdb=" O ALA J 224 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 286 through 288 Processing sheet with id=AE9, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.851A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR K 133 " --> pdb=" O VAL K 103 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET K 132 " --> pdb=" O ILE K 357 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 176 through 178 removed outlier: 6.343A pdb=" N THR K 297 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AF3, first strand: chain 'N' and resid 301 through 302 1642 hydrogen bonds defined for protein. 4629 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: 8.38 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6780 1.32 - 1.44: 9572 1.44 - 1.57: 22951 1.57 - 1.69: 27 1.69 - 1.81: 338 Bond restraints: 39668 Sorted by residual: bond pdb=" C ARG D 400 " pdb=" O ARG D 400 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.17e-02 7.31e+03 9.68e+00 bond pdb=" N GLY I 8 " pdb=" CA GLY I 8 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.36e+00 bond pdb=" CZ ARG D 400 " pdb=" NH1 ARG D 400 " ideal model delta sigma weight residual 1.323 1.350 -0.027 1.40e-02 5.10e+03 3.81e+00 bond pdb=" N TYR G 58 " pdb=" CA TYR G 58 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N GLN H 738 " pdb=" CA GLN H 738 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 ... (remaining 39663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 52829 1.69 - 3.37: 559 3.37 - 5.06: 158 5.06 - 6.74: 42 6.74 - 8.43: 7 Bond angle restraints: 53595 Sorted by residual: angle pdb=" N GLY J 353 " pdb=" CA GLY J 353 " pdb=" C GLY J 353 " ideal model delta sigma weight residual 112.73 120.10 -7.37 1.20e+00 6.94e-01 3.77e+01 angle pdb=" N THR J 355 " pdb=" CA THR J 355 " pdb=" C THR J 355 " ideal model delta sigma weight residual 111.71 116.80 -5.09 1.15e+00 7.56e-01 1.96e+01 angle pdb=" N SER J 20 " pdb=" CA SER J 20 " pdb=" C SER J 20 " ideal model delta sigma weight residual 111.28 115.46 -4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N ILE F 250 " pdb=" CA ILE F 250 " pdb=" C ILE F 250 " ideal model delta sigma weight residual 111.91 109.10 2.81 8.90e-01 1.26e+00 9.94e+00 angle pdb=" C2' ADP B 501 " pdb=" C3' ADP B 501 " pdb=" C4' ADP B 501 " ideal model delta sigma weight residual 111.00 102.57 8.43 3.00e+00 1.11e-01 7.90e+00 ... (remaining 53590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.35: 23923 25.35 - 50.69: 321 50.69 - 76.04: 22 76.04 - 101.39: 6 101.39 - 126.73: 1 Dihedral angle restraints: 24273 sinusoidal: 10074 harmonic: 14199 Sorted by residual: dihedral pdb=" O2A ADP A 501 " pdb=" O3A ADP A 501 " pdb=" PA ADP A 501 " pdb=" PB ADP A 501 " ideal model delta sinusoidal sigma weight residual -60.00 66.73 -126.73 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" O2A ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PA ADP D 501 " pdb=" PB ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 26.76 -86.76 1 2.00e+01 2.50e-03 2.26e+01 dihedral pdb=" C2' ADP K 401 " pdb=" C1' ADP K 401 " pdb=" N9 ADP K 401 " pdb=" C4 ADP K 401 " ideal model delta sinusoidal sigma weight residual 91.55 171.89 -80.34 1 2.00e+01 2.50e-03 2.00e+01 ... (remaining 24270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 5364 0.060 - 0.119: 670 0.119 - 0.179: 44 0.179 - 0.239: 3 0.239 - 0.299: 3 Chirality restraints: 6084 Sorted by residual: chirality pdb=" C1' ADP C 501 " pdb=" C2' ADP C 501 " pdb=" N9 ADP C 501 " pdb=" O4' ADP C 501 " both_signs ideal model delta sigma weight residual False 2.48 2.19 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' ADP C 501 " pdb=" C1' ADP C 501 " pdb=" C3' ADP C 501 " pdb=" O2' ADP C 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.80 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA SER J 20 " pdb=" N SER J 20 " pdb=" C SER J 20 " pdb=" CB SER J 20 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 6081 not shown) Planarity restraints: 6846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER J 20 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C SER J 20 " -0.038 2.00e-02 2.50e+03 pdb=" O SER J 20 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR J 21 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 265 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO E 266 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 266 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 266 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 69 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.23e+00 pdb=" N PRO G 70 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO G 70 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO G 70 " -0.021 5.00e-02 4.00e+02 ... (remaining 6843 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 142 2.39 - 3.02: 24607 3.02 - 3.65: 58356 3.65 - 4.27: 88562 4.27 - 4.90: 146654 Nonbonded interactions: 318321 Sorted by model distance: nonbonded pdb=" OD1 ASP K 157 " pdb=" C4' ADP K 401 " model vdw 1.765 3.470 nonbonded pdb=" OG1 THR B 165 " pdb=" O MET B 168 " model vdw 1.989 3.040 nonbonded pdb=" O ARG H1880 " pdb=" OG1 THR H1951 " model vdw 1.993 3.040 nonbonded pdb=" OD1 ASP K 157 " pdb=" O5' ADP K 401 " model vdw 1.997 3.040 nonbonded pdb=" OE2 GLU E 105 " pdb=" OG1 THR F 265 " model vdw 2.023 3.040 ... (remaining 318316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 140 or resid 155 through 193 or resid 199 throu \ gh 446 or resid 501)) selection = (chain 'C' and resid 13 through 501) selection = (chain 'E' and (resid 13 through 140 or resid 155 through 193 or resid 199 throu \ gh 501)) } ncs_group { reference = (chain 'B' and (resid 18 through 94 or resid 98 through 146 or resid 159 through \ 447 or resid 501)) selection = (chain 'D' and (resid 18 through 94 or resid 98 through 146 or resid 159 through \ 183 or resid 191 through 202 or resid 226 through 447 or resid 501)) selection = (chain 'F' and (resid 18 through 183 or resid 191 through 202 or resid 226 throu \ gh 501)) } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 8 through 215 or resid 246 through 284 or resid 293 throug \ h 417 or resid 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 32.180 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5606 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 : 0.011 0.875 39679 Z= 1.116 Angle : 0.516 8.430 53595 Z= 0.277 Chirality : 0.040 0.299 6084 Planarity : 0.002 0.044 6846 Dihedral : 8.615 126.733 15103 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.14 % Allowed : 3.65 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.11), residues: 4848 helix: -0.45 (0.11), residues: 2035 sheet: -1.87 (0.17), residues: 687 loop : -2.18 (0.12), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 400 TYR 0.009 0.001 TYR J 21 PHE 0.007 0.001 PHE B 257 TRP 0.008 0.001 TRP H1970 HIS 0.003 0.000 HIS A 316 Details of bonding type rmsd covalent geometry : bond 0.00206 (39668) covalent geometry : angle 0.51584 (53595) hydrogen bonds : bond 0.17115 ( 1642) hydrogen bonds : angle 6.14434 ( 4629) Misc. bond : bond 0.66658 ( 11) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1058 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8081 (mmm) cc_final: 0.7541 (mmm) REVERT: A 249 ARG cc_start: 0.6207 (ptm-80) cc_final: 0.5730 (mmm-85) REVERT: A 286 TYR cc_start: 0.7859 (m-80) cc_final: 0.7601 (m-80) REVERT: A 293 GLU cc_start: 0.7857 (tt0) cc_final: 0.7193 (tm-30) REVERT: A 332 ASN cc_start: 0.7561 (t0) cc_final: 0.6851 (m110) REVERT: A 364 MET cc_start: 0.6747 (mmm) cc_final: 0.6224 (mmm) REVERT: A 415 LEU cc_start: 0.7140 (tp) cc_final: 0.6918 (mt) REVERT: A 422 LYS cc_start: 0.6558 (mmtt) cc_final: 0.6332 (mmtp) REVERT: B 136 GLU cc_start: 0.6413 (mt-10) cc_final: 0.5834 (mp0) REVERT: B 169 GLU cc_start: 0.5779 (mt-10) cc_final: 0.4905 (pp20) REVERT: B 338 THR cc_start: 0.7721 (p) cc_final: 0.7520 (p) REVERT: B 353 ARG cc_start: 0.5612 (mmt180) cc_final: 0.5030 (ttm170) REVERT: B 392 ARG cc_start: 0.7701 (ttp-170) cc_final: 0.7208 (ttm-80) REVERT: C 27 ASP cc_start: 0.7591 (m-30) cc_final: 0.7322 (m-30) REVERT: C 229 HIS cc_start: 0.7361 (t-170) cc_final: 0.7110 (t70) REVERT: C 232 LYS cc_start: 0.7001 (pttt) cc_final: 0.6729 (tttp) REVERT: C 234 ILE cc_start: 0.8164 (mt) cc_final: 0.7791 (pt) REVERT: C 237 ASP cc_start: 0.7261 (m-30) cc_final: 0.6949 (t0) REVERT: C 244 ASP cc_start: 0.7830 (m-30) cc_final: 0.7485 (m-30) REVERT: C 255 ASP cc_start: 0.6786 (p0) cc_final: 0.6339 (p0) REVERT: C 273 ASP cc_start: 0.6863 (t70) cc_final: 0.6213 (t0) REVERT: C 346 SER cc_start: 0.8657 (m) cc_final: 0.8426 (t) REVERT: D 164 LYS cc_start: 0.6703 (tmtt) cc_final: 0.6478 (tmtt) REVERT: D 178 MET cc_start: 0.7819 (tpt) cc_final: 0.7573 (tpt) REVERT: D 303 MET cc_start: 0.8210 (mmp) cc_final: 0.7973 (mmp) REVERT: D 340 TYR cc_start: 0.7555 (p90) cc_final: 0.7120 (p90) REVERT: D 348 ILE cc_start: 0.7388 (mt) cc_final: 0.7059 (mp) REVERT: D 352 ASP cc_start: 0.6145 (t0) cc_final: 0.5904 (m-30) REVERT: D 362 TYR cc_start: 0.5803 (m-80) cc_final: 0.5577 (m-80) REVERT: E 61 MET cc_start: 0.7842 (mmm) cc_final: 0.7485 (mmm) REVERT: E 90 LYS cc_start: 0.7860 (mmmt) cc_final: 0.7657 (ptmt) REVERT: E 126 GLU cc_start: 0.6834 (tp30) cc_final: 0.6607 (mt-10) REVERT: E 182 LYS cc_start: 0.8095 (tptt) cc_final: 0.7671 (ttmt) REVERT: E 189 ASP cc_start: 0.8537 (p0) cc_final: 0.7912 (p0) REVERT: E 194 GLU cc_start: 0.6574 (mt-10) cc_final: 0.6245 (mm-30) REVERT: E 201 LYS cc_start: 0.6742 (mttp) cc_final: 0.5813 (tptt) REVERT: E 225 LYS cc_start: 0.8037 (mtpt) cc_final: 0.7837 (mtpt) REVERT: E 231 LYS cc_start: 0.7070 (tttt) cc_final: 0.6644 (tttt) REVERT: E 333 ARG cc_start: 0.5853 (mtt180) cc_final: 0.5332 (mmt180) REVERT: E 424 SER cc_start: 0.8113 (m) cc_final: 0.7887 (t) REVERT: F 231 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7265 (mm-30) REVERT: F 234 LYS cc_start: 0.6574 (tttt) cc_final: 0.6366 (ptpp) REVERT: F 251 ASN cc_start: 0.7130 (t0) cc_final: 0.6807 (t0) REVERT: F 269 LYS cc_start: 0.7156 (tppt) cc_final: 0.6364 (ttmt) REVERT: F 285 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6084 (mm-30) REVERT: F 441 GLN cc_start: 0.6500 (mm-40) cc_final: 0.6080 (tm-30) REVERT: F 442 TYR cc_start: 0.6747 (m-80) cc_final: 0.6116 (m-10) REVERT: G 62 TYR cc_start: 0.7195 (m-80) cc_final: 0.6802 (m-80) REVERT: G 96 LYS cc_start: 0.7462 (tttt) cc_final: 0.7059 (tttp) REVERT: G 110 MET cc_start: 0.5464 (ttp) cc_final: 0.5251 (tpp) REVERT: G 115 ARG cc_start: 0.7291 (mmp-170) cc_final: 0.6849 (mmp-170) REVERT: G 254 ILE cc_start: 0.6041 (mt) cc_final: 0.5663 (tt) REVERT: G 255 GLU cc_start: 0.7962 (tp30) cc_final: 0.7752 (tp30) REVERT: G 261 ARG cc_start: 0.6336 (ttt-90) cc_final: 0.5987 (mmt-90) REVERT: H 845 TRP cc_start: 0.4658 (m100) cc_final: 0.3449 (t60) REVERT: H 1284 TYR cc_start: 0.4786 (m-80) cc_final: 0.4499 (m-80) REVERT: H 1330 ARG cc_start: 0.6818 (ttm170) cc_final: 0.6554 (ttm170) REVERT: H 1365 GLU cc_start: 0.6986 (mt-10) cc_final: 0.6708 (tt0) REVERT: H 1388 ARG cc_start: 0.6186 (mtm110) cc_final: 0.5613 (mtt90) REVERT: H 1398 LYS cc_start: 0.7857 (mttt) cc_final: 0.7473 (mmtt) REVERT: H 1890 MET cc_start: 0.7981 (tpt) cc_final: 0.7532 (tpt) REVERT: H 1945 ASN cc_start: 0.6186 (p0) cc_final: 0.5976 (p0) REVERT: H 1991 ILE cc_start: 0.5028 (pt) cc_final: 0.4807 (pt) REVERT: H 2016 MET cc_start: 0.6570 (tpp) cc_final: 0.6283 (ttt) REVERT: H 2018 PHE cc_start: 0.5001 (m-10) cc_final: 0.4644 (m-80) REVERT: I 68 TYR cc_start: 0.1685 (m-80) cc_final: 0.1452 (p90) REVERT: I 96 TRP cc_start: 0.1875 (m100) cc_final: 0.1662 (m100) REVERT: I 166 THR cc_start: 0.6023 (p) cc_final: 0.5347 (m) REVERT: I 213 MET cc_start: 0.1129 (mpt) cc_final: 0.0542 (ptm) REVERT: I 254 MET cc_start: 0.3410 (mmp) cc_final: 0.3037 (mmt) REVERT: I 282 MET cc_start: 0.3605 (ppp) cc_final: 0.3323 (ptm) REVERT: I 323 LEU cc_start: 0.5995 (mp) cc_final: 0.5732 (pt) REVERT: I 331 THR cc_start: 0.4398 (p) cc_final: 0.4181 (m) REVERT: J 70 ILE cc_start: 0.5763 (tp) cc_final: 0.4784 (tp) REVERT: J 88 LEU cc_start: 0.8298 (mp) cc_final: 0.8066 (mp) REVERT: J 92 MET cc_start: 0.6121 (mmp) cc_final: 0.5508 (mmm) REVERT: J 109 MET cc_start: 0.7721 (mmp) cc_final: 0.7475 (mmt) REVERT: J 222 MET cc_start: 0.6272 (mtp) cc_final: 0.4912 (tpt) REVERT: J 364 LEU cc_start: 0.7433 (tp) cc_final: 0.6971 (mt) REVERT: K 16 MET cc_start: 0.6632 (ptp) cc_final: 0.6269 (ptp) REVERT: K 25 ASP cc_start: 0.7343 (m-30) cc_final: 0.6802 (p0) REVERT: K 34 ILE cc_start: 0.8313 (tt) cc_final: 0.8095 (tp) REVERT: K 78 ASN cc_start: 0.7896 (p0) cc_final: 0.7192 (p0) REVERT: K 100 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7614 (pt0) REVERT: K 128 ASN cc_start: 0.7449 (t0) cc_final: 0.7240 (t0) REVERT: K 208 ILE cc_start: 0.7859 (mp) cc_final: 0.7506 (mt) REVERT: K 263 GLN cc_start: 0.6942 (mt0) cc_final: 0.6645 (tt0) REVERT: K 358 SER cc_start: 0.8441 (t) cc_final: 0.8126 (m) REVERT: M 444 THR cc_start: 0.7933 (m) cc_final: 0.7341 (m) REVERT: M 482 ASP cc_start: 0.5698 (t70) cc_final: 0.5154 (p0) REVERT: N 204 LYS cc_start: 0.3948 (mttt) cc_final: 0.3597 (ptpt) REVERT: N 269 SER cc_start: 0.8021 (t) cc_final: 0.7214 (p) REVERT: N 303 ASP cc_start: 0.7812 (t0) cc_final: 0.7441 (t0) REVERT: N 305 VAL cc_start: 0.7156 (t) cc_final: 0.6906 (m) outliers start: 6 outliers final: 2 residues processed: 1064 average time/residue: 0.2417 time to fit residues: 402.9301 Evaluate side-chains 573 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 571 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain H residue 1749 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 0.0970 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 470 optimal weight: 0.1980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 44 ASN A 380 GLN A 385 ASN A 408 GLN B 49 GLN B 146 GLN C 13 GLN C 181 GLN C 262 GLN C 392 ASN C 420 ASN D 25 HIS D 49 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN E 115 ASN E 254 GLN E 332 ASN F 226 GLN F 255 GLN F 277 ASN G 229 GLN H 792 GLN H1261 HIS H1320 ASN H1827 GLN H1850 GLN H1858 GLN ** H1998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H2010 GLN I 263 GLN I 383 ASN ** J 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 190 GLN J 251 HIS K 111 ASN K 360 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.178226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.140015 restraints weight = 59525.386| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.80 r_work: 0.3469 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39679 Z= 0.133 Angle : 0.626 8.736 53595 Z= 0.304 Chirality : 0.044 0.230 6084 Planarity : 0.005 0.063 6846 Dihedral : 5.585 140.231 5452 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.64 % Allowed : 9.65 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.12), residues: 4848 helix: 0.64 (0.12), residues: 2058 sheet: -1.41 (0.18), residues: 720 loop : -1.64 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 439 TYR 0.023 0.001 TYR G 246 PHE 0.026 0.002 PHE I 262 TRP 0.023 0.001 TRP I 394 HIS 0.009 0.001 HIS G 113 Details of bonding type rmsd covalent geometry : bond 0.00304 (39668) covalent geometry : angle 0.62591 (53595) hydrogen bonds : bond 0.03677 ( 1642) hydrogen bonds : angle 4.70250 ( 4629) Misc. bond : bond 0.00265 ( 11) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 609 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8216 (mp0) REVERT: A 422 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7711 (mttm) REVERT: B 169 GLU cc_start: 0.5317 (mt-10) cc_final: 0.4661 (pp20) REVERT: B 267 GLU cc_start: 0.6437 (pt0) cc_final: 0.5405 (mm-30) REVERT: B 282 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7400 (mt-10) REVERT: B 353 ARG cc_start: 0.6392 (mmt180) cc_final: 0.6147 (mtm-85) REVERT: B 392 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.8285 (ttm-80) REVERT: B 442 TYR cc_start: 0.7617 (m-10) cc_final: 0.7307 (m-10) REVERT: C 244 ASP cc_start: 0.8146 (m-30) cc_final: 0.7890 (m-30) REVERT: C 364 MET cc_start: 0.7787 (mpp) cc_final: 0.7394 (mpp) REVERT: C 378 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6592 (tpm-80) REVERT: D 180 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7638 (mm-30) REVERT: D 303 MET cc_start: 0.9103 (mmp) cc_final: 0.8892 (mmp) REVERT: D 352 ASP cc_start: 0.6390 (t0) cc_final: 0.6178 (m-30) REVERT: D 378 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7041 (mt-10) REVERT: E 61 MET cc_start: 0.8532 (mmm) cc_final: 0.8236 (mmm) REVERT: E 201 LYS cc_start: 0.7003 (mttp) cc_final: 0.6603 (tptt) REVERT: E 265 LYS cc_start: 0.7299 (tttt) cc_final: 0.7047 (tttp) REVERT: F 132 LYS cc_start: 0.8286 (ptpt) cc_final: 0.7904 (mtmt) REVERT: F 269 LYS cc_start: 0.7979 (tppt) cc_final: 0.7674 (ttmt) REVERT: G 140 GLU cc_start: 0.7439 (tt0) cc_final: 0.7136 (pm20) REVERT: G 168 ASP cc_start: 0.6934 (m-30) cc_final: 0.6604 (m-30) REVERT: G 261 ARG cc_start: 0.6423 (ttt-90) cc_final: 0.6085 (mpt180) REVERT: G 264 ARG cc_start: 0.2810 (mtp180) cc_final: 0.2599 (mtp180) REVERT: H 845 TRP cc_start: 0.4947 (m100) cc_final: 0.3879 (t60) REVERT: H 1118 LYS cc_start: 0.4585 (mttt) cc_final: 0.4056 (tppt) REVERT: H 1185 MET cc_start: 0.2599 (mmp) cc_final: 0.1085 (tmm) REVERT: H 1388 ARG cc_start: 0.6492 (mtm110) cc_final: 0.6246 (mtt90) REVERT: H 1781 LEU cc_start: 0.6558 (mt) cc_final: 0.5770 (mt) REVERT: H 1890 MET cc_start: 0.8625 (tpt) cc_final: 0.8201 (tpt) REVERT: I 68 TYR cc_start: 0.2226 (m-80) cc_final: 0.1864 (p90) REVERT: I 96 TRP cc_start: 0.1481 (m100) cc_final: 0.1261 (m100) REVERT: I 152 CYS cc_start: 0.6909 (p) cc_final: 0.6489 (p) REVERT: I 205 GLN cc_start: 0.3492 (mp10) cc_final: 0.2813 (mt0) REVERT: I 213 MET cc_start: 0.1001 (mpt) cc_final: 0.0356 (mmt) REVERT: I 282 MET cc_start: 0.3076 (ppp) cc_final: 0.2671 (ptm) REVERT: I 322 MET cc_start: -0.1169 (tpt) cc_final: -0.1622 (tpt) REVERT: J 43 MET cc_start: 0.5933 (tmm) cc_final: 0.4691 (ttt) REVERT: J 95 ASP cc_start: 0.6748 (t0) cc_final: 0.6536 (t0) REVERT: J 250 TRP cc_start: 0.7266 (t-100) cc_final: 0.6671 (t-100) REVERT: J 335 MET cc_start: 0.7162 (mtp) cc_final: 0.6471 (mtt) REVERT: J 364 LEU cc_start: 0.7937 (tp) cc_final: 0.7534 (mt) REVERT: K 208 ILE cc_start: 0.7812 (mp) cc_final: 0.7596 (mt) REVERT: K 217 CYS cc_start: 0.6842 (t) cc_final: 0.6534 (m) REVERT: K 313 MET cc_start: 0.8970 (tpt) cc_final: 0.8753 (tpp) REVERT: M 482 ASP cc_start: 0.5631 (t70) cc_final: 0.5225 (p0) REVERT: N 204 LYS cc_start: 0.4127 (mttt) cc_final: 0.3833 (ptpt) REVERT: N 269 SER cc_start: 0.8009 (t) cc_final: 0.7666 (p) outliers start: 69 outliers final: 36 residues processed: 653 average time/residue: 0.2242 time to fit residues: 234.0401 Evaluate side-chains 497 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 459 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 203 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 164 SER Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1736 LEU Chi-restraints excluded: chain H residue 1739 CYS Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain J residue 339 ASP Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 373 optimal weight: 40.0000 chunk 379 optimal weight: 0.9990 chunk 442 optimal weight: 4.9990 chunk 390 optimal weight: 20.0000 chunk 414 optimal weight: 0.0020 chunk 303 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 483 optimal weight: 30.0000 chunk 9 optimal weight: 0.9980 chunk 172 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN D 240 HIS E 332 ASN E 393 HIS F 188 GLN G 229 GLN H1279 GLN J 118 HIS J 128 ASN K 12 ASN K 263 GLN K 275 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.174891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.135696 restraints weight = 58715.970| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.98 r_work: 0.3400 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 39679 Z= 0.125 Angle : 0.593 8.869 53595 Z= 0.289 Chirality : 0.043 0.292 6084 Planarity : 0.004 0.057 6846 Dihedral : 5.520 138.530 5450 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.06 % Allowed : 11.40 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.12), residues: 4848 helix: 1.04 (0.12), residues: 2043 sheet: -1.17 (0.18), residues: 713 loop : -1.41 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H1810 TYR 0.025 0.001 TYR H1836 PHE 0.027 0.002 PHE B 257 TRP 0.023 0.001 TRP I 394 HIS 0.009 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00288 (39668) covalent geometry : angle 0.59324 (53595) hydrogen bonds : bond 0.03283 ( 1642) hydrogen bonds : angle 4.42646 ( 4629) Misc. bond : bond 0.00225 ( 11) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 501 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: A 171 LYS cc_start: 0.6324 (mttm) cc_final: 0.6116 (mttp) REVERT: A 364 MET cc_start: 0.8110 (mmt) cc_final: 0.7840 (mtm) REVERT: B 169 GLU cc_start: 0.5468 (mt-10) cc_final: 0.4887 (pp20) REVERT: B 267 GLU cc_start: 0.6421 (pt0) cc_final: 0.5403 (mm-30) REVERT: B 282 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7407 (mt-10) REVERT: B 353 ARG cc_start: 0.6619 (mmt180) cc_final: 0.6268 (mtt-85) REVERT: B 369 GLN cc_start: 0.8575 (tp40) cc_final: 0.8336 (tp-100) REVERT: B 442 TYR cc_start: 0.8003 (m-10) cc_final: 0.7782 (m-10) REVERT: C 171 LYS cc_start: 0.7563 (mtmm) cc_final: 0.6808 (mttt) REVERT: C 244 ASP cc_start: 0.8219 (m-30) cc_final: 0.7830 (m-30) REVERT: C 274 LYS cc_start: 0.8859 (ttpp) cc_final: 0.8363 (ttpp) REVERT: C 378 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.6782 (tpm-80) REVERT: C 418 LYS cc_start: 0.8534 (mttt) cc_final: 0.8320 (mtpp) REVERT: D 269 LYS cc_start: 0.8382 (tptt) cc_final: 0.8087 (tptp) REVERT: D 352 ASP cc_start: 0.6471 (t0) cc_final: 0.6130 (m-30) REVERT: E 237 ASP cc_start: 0.8074 (p0) cc_final: 0.7633 (p0) REVERT: E 242 ASP cc_start: 0.7969 (m-30) cc_final: 0.7759 (m-30) REVERT: E 377 ILE cc_start: 0.8584 (tt) cc_final: 0.7960 (mt) REVERT: F 132 LYS cc_start: 0.8436 (ptpt) cc_final: 0.8057 (mtmt) REVERT: F 195 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8257 (pt) REVERT: F 269 LYS cc_start: 0.8061 (tppt) cc_final: 0.7603 (ttmt) REVERT: G 60 LEU cc_start: 0.6170 (OUTLIER) cc_final: 0.5763 (mp) REVERT: G 140 GLU cc_start: 0.7327 (tt0) cc_final: 0.6861 (pm20) REVERT: G 168 ASP cc_start: 0.6943 (m-30) cc_final: 0.6739 (m-30) REVERT: G 261 ARG cc_start: 0.6385 (ttt-90) cc_final: 0.6056 (mpt180) REVERT: G 264 ARG cc_start: 0.2973 (mtp180) cc_final: 0.2543 (mtm180) REVERT: H 830 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7477 (tm) REVERT: H 845 TRP cc_start: 0.4985 (m100) cc_final: 0.3497 (t60) REVERT: H 1118 LYS cc_start: 0.4576 (mttt) cc_final: 0.4147 (tppt) REVERT: H 1185 MET cc_start: 0.2282 (mmp) cc_final: 0.1188 (tmm) REVERT: H 1191 MET cc_start: 0.3038 (mtt) cc_final: 0.1881 (pmm) REVERT: H 1225 MET cc_start: 0.3495 (tpp) cc_final: 0.3079 (tpp) REVERT: H 1890 MET cc_start: 0.8604 (tpt) cc_final: 0.8179 (tpt) REVERT: I 96 TRP cc_start: 0.1557 (m100) cc_final: 0.1356 (m100) REVERT: I 109 MET cc_start: 0.4686 (mmm) cc_final: 0.4312 (ptp) REVERT: I 152 CYS cc_start: 0.7133 (p) cc_final: 0.6690 (p) REVERT: I 213 MET cc_start: 0.0923 (mpt) cc_final: 0.0426 (mmt) REVERT: I 282 MET cc_start: 0.2837 (ppp) cc_final: 0.2626 (ptm) REVERT: J 43 MET cc_start: 0.5935 (tmm) cc_final: 0.5094 (ttt) REVERT: J 82 MET cc_start: 0.5317 (ttt) cc_final: 0.4853 (tmm) REVERT: J 95 ASP cc_start: 0.6711 (t0) cc_final: 0.6430 (t0) REVERT: J 222 MET cc_start: 0.5992 (OUTLIER) cc_final: 0.5421 (tpt) REVERT: J 335 MET cc_start: 0.7121 (mtp) cc_final: 0.6612 (mtt) REVERT: J 348 VAL cc_start: 0.8013 (t) cc_final: 0.7132 (m) REVERT: J 364 LEU cc_start: 0.8030 (tp) cc_final: 0.7558 (mt) REVERT: K 208 ILE cc_start: 0.7933 (mp) cc_final: 0.7711 (mt) REVERT: K 313 MET cc_start: 0.8917 (tpt) cc_final: 0.8705 (tpp) REVERT: K 315 LYS cc_start: 0.8094 (ttmm) cc_final: 0.7821 (mtmt) REVERT: M 482 ASP cc_start: 0.5509 (t70) cc_final: 0.5195 (p0) REVERT: N 204 LYS cc_start: 0.4301 (mttt) cc_final: 0.3898 (ptpt) REVERT: N 269 SER cc_start: 0.8196 (t) cc_final: 0.7883 (p) outliers start: 87 outliers final: 43 residues processed: 558 average time/residue: 0.2234 time to fit residues: 202.1664 Evaluate side-chains 479 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 430 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1323 SER Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1810 ARG Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain H residue 1825 LEU Chi-restraints excluded: chain H residue 2230 MET Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 266 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 437 optimal weight: 0.6980 chunk 112 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS B 344 HIS C 18 HIS C 20 HIS D 240 HIS ** E 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS G 130 ASN G 229 GLN H1156 HIS I 176 HIS J 110 HIS J 118 HIS K 12 ASN M 449 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.171478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.131273 restraints weight = 58149.785| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.16 r_work: 0.3323 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39679 Z= 0.140 Angle : 0.602 9.569 53595 Z= 0.292 Chirality : 0.044 0.286 6084 Planarity : 0.005 0.076 6846 Dihedral : 5.605 141.629 5450 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.65 % Allowed : 11.64 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.12), residues: 4848 helix: 1.07 (0.12), residues: 2060 sheet: -0.93 (0.18), residues: 723 loop : -1.32 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 341 TYR 0.025 0.001 TYR H1836 PHE 0.019 0.002 PHE I 262 TRP 0.019 0.001 TRP I 394 HIS 0.010 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00329 (39668) covalent geometry : angle 0.60211 (53595) hydrogen bonds : bond 0.03365 ( 1642) hydrogen bonds : angle 4.33940 ( 4629) Misc. bond : bond 0.00235 ( 11) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 455 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8251 (mp0) REVERT: A 259 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5444 (ptp) REVERT: B 90 MET cc_start: 0.8695 (ttm) cc_final: 0.8351 (mtp) REVERT: B 169 GLU cc_start: 0.5561 (mt-10) cc_final: 0.4920 (pp20) REVERT: B 267 GLU cc_start: 0.6707 (pt0) cc_final: 0.5482 (mm-30) REVERT: B 354 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8926 (pp) REVERT: C 171 LYS cc_start: 0.7524 (mtmm) cc_final: 0.6853 (mttt) REVERT: C 244 ASP cc_start: 0.8325 (m-30) cc_final: 0.7970 (m-30) REVERT: C 274 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8574 (ttpp) REVERT: C 378 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.7175 (tpm-80) REVERT: D 180 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7544 (mm-30) REVERT: D 269 LYS cc_start: 0.8520 (tptt) cc_final: 0.7617 (tptp) REVERT: E 18 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7628 (p90) REVERT: E 61 MET cc_start: 0.8969 (mmm) cc_final: 0.8731 (mmm) REVERT: E 237 ASP cc_start: 0.8178 (p0) cc_final: 0.7947 (p0) REVERT: E 260 MET cc_start: 0.3503 (ttt) cc_final: 0.2872 (ttt) REVERT: E 274 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8255 (tmmm) REVERT: E 316 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7343 (p-80) REVERT: E 377 ILE cc_start: 0.8599 (tt) cc_final: 0.8206 (mt) REVERT: F 132 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8045 (mtmt) REVERT: F 195 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8355 (pt) REVERT: F 269 LYS cc_start: 0.8154 (tppt) cc_final: 0.7731 (ttmt) REVERT: G 60 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.5938 (mp) REVERT: G 98 MET cc_start: 0.8085 (ptp) cc_final: 0.7857 (ptp) REVERT: G 140 GLU cc_start: 0.7204 (tt0) cc_final: 0.6835 (pm20) REVERT: G 168 ASP cc_start: 0.6925 (m-30) cc_final: 0.6701 (m-30) REVERT: G 231 GLU cc_start: 0.6964 (pt0) cc_final: 0.6557 (tm-30) REVERT: G 255 GLU cc_start: 0.7636 (tp30) cc_final: 0.7415 (tp30) REVERT: G 261 ARG cc_start: 0.6392 (ttt-90) cc_final: 0.6056 (mpt180) REVERT: G 264 ARG cc_start: 0.3245 (mtp180) cc_final: 0.2818 (mtm180) REVERT: H 830 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7450 (tm) REVERT: H 845 TRP cc_start: 0.5229 (m100) cc_final: 0.3689 (t60) REVERT: H 1118 LYS cc_start: 0.4401 (mttt) cc_final: 0.3942 (tppt) REVERT: H 1185 MET cc_start: 0.1832 (mmp) cc_final: 0.1150 (tmm) REVERT: H 1191 MET cc_start: 0.3014 (mtt) cc_final: 0.1869 (pmm) REVERT: H 1325 LEU cc_start: 0.8087 (mt) cc_final: 0.7742 (mt) REVERT: H 1327 ARG cc_start: 0.5122 (mtp180) cc_final: 0.4691 (mtt180) REVERT: H 1797 PHE cc_start: 0.6490 (m-10) cc_final: 0.6133 (m-10) REVERT: H 1836 TYR cc_start: 0.6483 (t80) cc_final: 0.5977 (t80) REVERT: H 1890 MET cc_start: 0.8668 (tpt) cc_final: 0.8251 (tpt) REVERT: H 2177 LEU cc_start: 0.7609 (tp) cc_final: 0.7314 (tp) REVERT: I 213 MET cc_start: 0.0712 (mpt) cc_final: 0.0374 (mmt) REVERT: I 409 MET cc_start: 0.6059 (mmp) cc_final: 0.5783 (tpp) REVERT: J 43 MET cc_start: 0.6006 (tmm) cc_final: 0.5442 (ttt) REVERT: J 82 MET cc_start: 0.5326 (ttt) cc_final: 0.4689 (ttm) REVERT: J 95 ASP cc_start: 0.6769 (t0) cc_final: 0.6569 (t0) REVERT: J 222 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5508 (tpt) REVERT: J 327 HIS cc_start: 0.7406 (m-70) cc_final: 0.7063 (m-70) REVERT: J 335 MET cc_start: 0.6989 (mtp) cc_final: 0.6451 (mtt) REVERT: J 348 VAL cc_start: 0.8067 (t) cc_final: 0.7790 (p) REVERT: K 208 ILE cc_start: 0.7920 (mp) cc_final: 0.7628 (mt) REVERT: K 240 TYR cc_start: 0.4764 (t80) cc_final: 0.4405 (t80) REVERT: K 313 MET cc_start: 0.9127 (tpt) cc_final: 0.8888 (tpp) REVERT: K 315 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7826 (mtmt) REVERT: N 204 LYS cc_start: 0.4141 (mttt) cc_final: 0.3741 (ptpt) REVERT: N 269 SER cc_start: 0.8353 (t) cc_final: 0.8025 (p) REVERT: N 275 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6451 (mp0) REVERT: N 339 LEU cc_start: 0.4093 (tt) cc_final: 0.3524 (mt) outliers start: 112 outliers final: 64 residues processed: 534 average time/residue: 0.2169 time to fit residues: 188.4059 Evaluate side-chains 473 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 397 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 259 MET Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 139 THR Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 18 HIS Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 316 HIS Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1323 SER Chi-restraints excluded: chain H residue 1326 VAL Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1810 ARG Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 250 TRP Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 471 HIS Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 275 GLU Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 235 optimal weight: 0.7980 chunk 356 optimal weight: 0.1980 chunk 122 optimal weight: 7.9990 chunk 280 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 361 optimal weight: 20.0000 chunk 177 optimal weight: 0.2980 chunk 278 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 321 optimal weight: 8.9990 chunk 343 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN B 302 HIS B 441 GLN D 226 GLN D 245 HIS E 305 HIS ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 229 GLN ** H1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1279 GLN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 118 HIS K 12 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.173526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.134078 restraints weight = 58077.485| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.97 r_work: 0.3368 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 39679 Z= 0.102 Angle : 0.563 8.918 53595 Z= 0.271 Chirality : 0.042 0.268 6084 Planarity : 0.004 0.065 6846 Dihedral : 5.362 136.685 5450 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.30 % Allowed : 12.68 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 4848 helix: 1.25 (0.12), residues: 2043 sheet: -0.82 (0.18), residues: 727 loop : -1.19 (0.14), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 252 TYR 0.020 0.001 TYR H1836 PHE 0.020 0.001 PHE I 262 TRP 0.018 0.001 TRP I 394 HIS 0.009 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00226 (39668) covalent geometry : angle 0.56271 (53595) hydrogen bonds : bond 0.02901 ( 1642) hydrogen bonds : angle 4.16521 ( 4629) Misc. bond : bond 0.00140 ( 11) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 437 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8264 (mp0) REVERT: A 364 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7983 (mmt) REVERT: B 169 GLU cc_start: 0.5621 (mt-10) cc_final: 0.4951 (pp20) REVERT: B 197 LYS cc_start: 0.3605 (mtpt) cc_final: 0.3354 (mtpt) REVERT: B 267 GLU cc_start: 0.5784 (pt0) cc_final: 0.4904 (mm-30) REVERT: B 354 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8902 (pp) REVERT: C 202 ARG cc_start: 0.7888 (tpt-90) cc_final: 0.7477 (tmt-80) REVERT: C 244 ASP cc_start: 0.8218 (m-30) cc_final: 0.7827 (m-30) REVERT: C 249 ARG cc_start: 0.8234 (ptm160) cc_final: 0.7868 (ttm-80) REVERT: C 274 LYS cc_start: 0.8909 (ttpp) cc_final: 0.8484 (ttpp) REVERT: C 378 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7931 (tpm-80) REVERT: D 180 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7602 (mm-30) REVERT: D 250 ILE cc_start: 0.7567 (mp) cc_final: 0.7363 (mt) REVERT: E 61 MET cc_start: 0.9021 (mmm) cc_final: 0.8761 (mmm) REVERT: E 260 MET cc_start: 0.3621 (ttt) cc_final: 0.2905 (ttt) REVERT: E 274 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7977 (tmmm) REVERT: E 377 ILE cc_start: 0.8566 (tt) cc_final: 0.8199 (mt) REVERT: F 136 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7248 (mm-30) REVERT: F 269 LYS cc_start: 0.8133 (tppt) cc_final: 0.7707 (ttmt) REVERT: F 376 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8219 (tt0) REVERT: G 60 LEU cc_start: 0.6239 (OUTLIER) cc_final: 0.5684 (mp) REVERT: G 140 GLU cc_start: 0.7313 (tt0) cc_final: 0.6964 (pm20) REVERT: G 231 GLU cc_start: 0.6957 (pt0) cc_final: 0.6512 (tm-30) REVERT: G 261 ARG cc_start: 0.6437 (ttt-90) cc_final: 0.6113 (mpt180) REVERT: G 264 ARG cc_start: 0.3395 (mtp180) cc_final: 0.3171 (mtm180) REVERT: H 830 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7499 (tm) REVERT: H 845 TRP cc_start: 0.5243 (m100) cc_final: 0.3780 (t60) REVERT: H 1118 LYS cc_start: 0.4550 (mttt) cc_final: 0.4061 (tppt) REVERT: H 1185 MET cc_start: 0.2129 (mmp) cc_final: 0.1518 (tmm) REVERT: H 1191 MET cc_start: 0.2969 (OUTLIER) cc_final: 0.1847 (pmm) REVERT: H 1327 ARG cc_start: 0.5331 (mtp180) cc_final: 0.4887 (mtt180) REVERT: H 1781 LEU cc_start: 0.6703 (mt) cc_final: 0.5337 (mp) REVERT: H 1836 TYR cc_start: 0.6268 (t80) cc_final: 0.5793 (t80) REVERT: H 1890 MET cc_start: 0.8615 (tpt) cc_final: 0.8218 (tpt) REVERT: H 2177 LEU cc_start: 0.7642 (tp) cc_final: 0.7364 (tp) REVERT: H 2193 TYR cc_start: 0.6477 (t80) cc_final: 0.5785 (t80) REVERT: I 152 CYS cc_start: 0.7192 (p) cc_final: 0.6800 (p) REVERT: I 213 MET cc_start: 0.0697 (mpt) cc_final: 0.0313 (mmt) REVERT: I 409 MET cc_start: 0.5738 (mmp) cc_final: 0.5470 (tpp) REVERT: J 43 MET cc_start: 0.5805 (tmm) cc_final: 0.5406 (ttt) REVERT: J 82 MET cc_start: 0.5590 (ttt) cc_final: 0.4943 (ttm) REVERT: J 95 ASP cc_start: 0.6758 (t0) cc_final: 0.6515 (t0) REVERT: J 222 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5434 (tpt) REVERT: J 327 HIS cc_start: 0.7375 (m-70) cc_final: 0.7017 (m-70) REVERT: J 335 MET cc_start: 0.6946 (mtp) cc_final: 0.6545 (mtt) REVERT: J 348 VAL cc_start: 0.7935 (t) cc_final: 0.7681 (p) REVERT: K 119 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8203 (ttm) REVERT: K 208 ILE cc_start: 0.8016 (mp) cc_final: 0.7759 (mt) REVERT: K 240 TYR cc_start: 0.4823 (t80) cc_final: 0.4444 (t80) REVERT: K 313 MET cc_start: 0.9096 (tpt) cc_final: 0.8893 (tpp) REVERT: K 315 LYS cc_start: 0.8143 (ttmm) cc_final: 0.7798 (mtmt) REVERT: M 411 GLN cc_start: 0.6292 (tt0) cc_final: 0.4835 (mt0) REVERT: M 478 PHE cc_start: 0.5680 (m-80) cc_final: 0.5449 (m-80) REVERT: N 204 LYS cc_start: 0.4130 (mttt) cc_final: 0.3680 (ptpt) REVERT: N 269 SER cc_start: 0.8255 (t) cc_final: 0.7981 (p) REVERT: N 275 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: N 339 LEU cc_start: 0.4718 (tt) cc_final: 0.4101 (mt) outliers start: 97 outliers final: 58 residues processed: 499 average time/residue: 0.2111 time to fit residues: 171.8700 Evaluate side-chains 446 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 377 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 285 LYS Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 274 LYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 202 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 836 SER Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1191 MET Chi-restraints excluded: chain H residue 1323 SER Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain H residue 2016 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 250 TRP Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 119 MET Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 275 GLU Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 245 optimal weight: 1.9990 chunk 258 optimal weight: 9.9990 chunk 47 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 438 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 384 optimal weight: 40.0000 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN D 226 GLN E 284 ASN F 245 HIS H1872 GLN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.168203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.128625 restraints weight = 58023.477| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.08 r_work: 0.3249 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39679 Z= 0.168 Angle : 0.633 9.170 53595 Z= 0.308 Chirality : 0.045 0.234 6084 Planarity : 0.005 0.068 6846 Dihedral : 5.715 147.378 5450 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.75 % Allowed : 12.94 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.12), residues: 4848 helix: 1.08 (0.12), residues: 2065 sheet: -0.78 (0.18), residues: 751 loop : -1.17 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H1847 TYR 0.021 0.001 TYR E 192 PHE 0.019 0.002 PHE B 257 TRP 0.018 0.001 TRP I 394 HIS 0.009 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00399 (39668) covalent geometry : angle 0.63260 (53595) hydrogen bonds : bond 0.03607 ( 1642) hydrogen bonds : angle 4.31285 ( 4629) Misc. bond : bond 0.00266 ( 11) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 411 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8602 (mm-30) REVERT: A 259 MET cc_start: 0.6856 (pmm) cc_final: 0.6476 (pmm) REVERT: B 90 MET cc_start: 0.8641 (ttm) cc_final: 0.8339 (mtp) REVERT: B 169 GLU cc_start: 0.6002 (mt-10) cc_final: 0.5192 (pp20) REVERT: B 267 GLU cc_start: 0.6033 (pt0) cc_final: 0.5116 (mm-30) REVERT: B 354 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8998 (pp) REVERT: C 244 ASP cc_start: 0.8291 (m-30) cc_final: 0.7922 (m-30) REVERT: C 249 ARG cc_start: 0.8357 (ptm160) cc_final: 0.7858 (ttm110) REVERT: C 274 LYS cc_start: 0.9000 (ttpp) cc_final: 0.8671 (ttpp) REVERT: C 308 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7627 (t0) REVERT: C 374 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8559 (mt) REVERT: C 378 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7257 (tpm-80) REVERT: D 180 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7574 (mm-30) REVERT: E 237 ASP cc_start: 0.8231 (p0) cc_final: 0.7896 (p0) REVERT: E 260 MET cc_start: 0.3715 (ttt) cc_final: 0.3090 (ttt) REVERT: F 269 LYS cc_start: 0.8270 (tppt) cc_final: 0.7814 (ttmt) REVERT: F 376 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8236 (tt0) REVERT: G 60 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5876 (mp) REVERT: G 140 GLU cc_start: 0.7207 (tt0) cc_final: 0.6933 (pm20) REVERT: G 231 GLU cc_start: 0.6976 (pt0) cc_final: 0.6420 (tm-30) REVERT: G 261 ARG cc_start: 0.6378 (ttt-90) cc_final: 0.6039 (mmt-90) REVERT: G 264 ARG cc_start: 0.3006 (mtp180) cc_final: 0.2623 (mtm180) REVERT: H 830 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7725 (tm) REVERT: H 845 TRP cc_start: 0.5207 (m100) cc_final: 0.3600 (t60) REVERT: H 1118 LYS cc_start: 0.4348 (mttt) cc_final: 0.3819 (tppt) REVERT: H 1185 MET cc_start: 0.1749 (mmp) cc_final: 0.1293 (tmm) REVERT: H 1191 MET cc_start: 0.3103 (mtt) cc_final: 0.1978 (pmm) REVERT: H 1225 MET cc_start: 0.2798 (tpp) cc_final: 0.2413 (tpp) REVERT: H 1836 TYR cc_start: 0.6277 (t80) cc_final: 0.6046 (t80) REVERT: H 1890 MET cc_start: 0.8876 (tpt) cc_final: 0.8439 (tpt) REVERT: H 2177 LEU cc_start: 0.7783 (tp) cc_final: 0.7506 (tp) REVERT: H 2193 TYR cc_start: 0.6674 (t80) cc_final: 0.6019 (t80) REVERT: I 213 MET cc_start: 0.0727 (mpt) cc_final: 0.0346 (mmt) REVERT: J 43 MET cc_start: 0.5889 (tmm) cc_final: 0.5528 (ttt) REVERT: J 82 MET cc_start: 0.6016 (ttt) cc_final: 0.5127 (ttm) REVERT: J 222 MET cc_start: 0.5951 (OUTLIER) cc_final: 0.5237 (tpt) REVERT: J 243 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7387 (tt) REVERT: J 327 HIS cc_start: 0.7402 (m-70) cc_final: 0.7050 (m-70) REVERT: J 335 MET cc_start: 0.7209 (mtp) cc_final: 0.6688 (mtt) REVERT: J 348 VAL cc_start: 0.8120 (t) cc_final: 0.7840 (p) REVERT: K 188 TYR cc_start: 0.7053 (t80) cc_final: 0.6840 (t80) REVERT: K 208 ILE cc_start: 0.8002 (mp) cc_final: 0.7737 (mt) REVERT: K 240 TYR cc_start: 0.4867 (t80) cc_final: 0.4452 (t80) REVERT: K 250 ILE cc_start: 0.7809 (mm) cc_final: 0.7456 (pt) REVERT: M 518 LEU cc_start: 0.2804 (OUTLIER) cc_final: 0.2450 (mm) REVERT: N 204 LYS cc_start: 0.3910 (mttt) cc_final: 0.3478 (ptpt) REVERT: N 269 SER cc_start: 0.8118 (t) cc_final: 0.7878 (p) REVERT: N 275 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6224 (mp0) outliers start: 116 outliers final: 75 residues processed: 487 average time/residue: 0.2231 time to fit residues: 179.8976 Evaluate side-chains 464 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 378 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 378 ARG Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 438 TYR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 435 ASP Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1310 GLN Chi-restraints excluded: chain H residue 1323 SER Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1399 ILE Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain H residue 1881 VAL Chi-restraints excluded: chain H residue 2186 THR Chi-restraints excluded: chain H residue 2211 LEU Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 122 MET Chi-restraints excluded: chain J residue 222 MET Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 250 TRP Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 436 VAL Chi-restraints excluded: chain M residue 471 HIS Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 275 GLU Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 246 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 356 optimal weight: 6.9990 chunk 416 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 chunk 288 optimal weight: 8.9990 chunk 308 optimal weight: 0.8980 chunk 222 optimal weight: 6.9990 chunk 236 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN D 226 GLN E 332 ASN H1832 HIS H1899 ASN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.170178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130968 restraints weight = 58089.356| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.14 r_work: 0.3286 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39679 Z= 0.115 Angle : 0.585 11.535 53595 Z= 0.282 Chirality : 0.042 0.217 6084 Planarity : 0.004 0.059 6846 Dihedral : 5.523 147.329 5450 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.16 % Allowed : 13.77 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.12), residues: 4848 helix: 1.28 (0.12), residues: 2039 sheet: -0.68 (0.18), residues: 737 loop : -1.07 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 205 TYR 0.028 0.001 TYR G 246 PHE 0.022 0.001 PHE F 261 TRP 0.022 0.001 TRP I 394 HIS 0.009 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00263 (39668) covalent geometry : angle 0.58509 (53595) hydrogen bonds : bond 0.03090 ( 1642) hydrogen bonds : angle 4.18383 ( 4629) Misc. bond : bond 0.00166 ( 11) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 401 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: A 259 MET cc_start: 0.6597 (pmm) cc_final: 0.6309 (pmm) REVERT: B 90 MET cc_start: 0.8681 (ttm) cc_final: 0.8349 (mtp) REVERT: B 116 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8670 (p) REVERT: B 169 GLU cc_start: 0.5888 (mt-10) cc_final: 0.5125 (pp20) REVERT: B 267 GLU cc_start: 0.5839 (pt0) cc_final: 0.5058 (mm-30) REVERT: B 354 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8979 (pp) REVERT: C 244 ASP cc_start: 0.8269 (m-30) cc_final: 0.7850 (m-30) REVERT: C 249 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7898 (ttm-80) REVERT: C 274 LYS cc_start: 0.8946 (ttpp) cc_final: 0.8598 (ttpp) REVERT: C 308 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7625 (t0) REVERT: C 374 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8531 (mt) REVERT: D 29 ARG cc_start: 0.7776 (ttm110) cc_final: 0.7499 (mtt-85) REVERT: E 61 MET cc_start: 0.9122 (mmm) cc_final: 0.8785 (mmm) REVERT: E 260 MET cc_start: 0.3698 (ttt) cc_final: 0.2970 (ttt) REVERT: E 265 LYS cc_start: 0.7250 (tttt) cc_final: 0.6787 (tmtt) REVERT: F 132 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7897 (pttt) REVERT: F 261 PHE cc_start: 0.7938 (p90) cc_final: 0.7731 (p90) REVERT: F 269 LYS cc_start: 0.8254 (tppt) cc_final: 0.7797 (ttmt) REVERT: F 376 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8185 (tt0) REVERT: G 60 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5832 (mp) REVERT: G 140 GLU cc_start: 0.7112 (tt0) cc_final: 0.6837 (pm20) REVERT: G 231 GLU cc_start: 0.6917 (pt0) cc_final: 0.6373 (tm-30) REVERT: G 261 ARG cc_start: 0.6394 (ttt-90) cc_final: 0.6127 (mpt180) REVERT: H 830 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7680 (tm) REVERT: H 845 TRP cc_start: 0.4982 (m100) cc_final: 0.3680 (t60) REVERT: H 1118 LYS cc_start: 0.4486 (mttt) cc_final: 0.3918 (tppt) REVERT: H 1185 MET cc_start: 0.1705 (mmp) cc_final: 0.1295 (tmm) REVERT: H 1191 MET cc_start: 0.2955 (mtt) cc_final: 0.1829 (pmm) REVERT: H 1225 MET cc_start: 0.3404 (tpp) cc_final: 0.2821 (tpp) REVERT: H 1327 ARG cc_start: 0.5612 (mtp180) cc_final: 0.5196 (mtt180) REVERT: H 1836 TYR cc_start: 0.6191 (t80) cc_final: 0.5982 (t80) REVERT: H 1890 MET cc_start: 0.8753 (tpt) cc_final: 0.8335 (tpt) REVERT: H 2177 LEU cc_start: 0.7791 (tp) cc_final: 0.7506 (tp) REVERT: H 2193 TYR cc_start: 0.6540 (t80) cc_final: 0.5892 (t80) REVERT: I 152 CYS cc_start: 0.7086 (p) cc_final: 0.6764 (p) REVERT: I 213 MET cc_start: 0.0867 (mpt) cc_final: 0.0386 (mmt) REVERT: J 68 TYR cc_start: 0.6266 (m-10) cc_final: 0.5683 (m-10) REVERT: J 82 MET cc_start: 0.6018 (ttt) cc_final: 0.5145 (ttm) REVERT: J 243 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7374 (tt) REVERT: J 251 HIS cc_start: 0.7350 (t-90) cc_final: 0.7035 (t-90) REVERT: J 327 HIS cc_start: 0.7354 (m-70) cc_final: 0.6992 (m-70) REVERT: J 335 MET cc_start: 0.6992 (mtp) cc_final: 0.6544 (mtt) REVERT: J 348 VAL cc_start: 0.7978 (t) cc_final: 0.7726 (p) REVERT: K 188 TYR cc_start: 0.7070 (t80) cc_final: 0.6828 (t80) REVERT: K 208 ILE cc_start: 0.7981 (mp) cc_final: 0.7715 (mt) REVERT: K 240 TYR cc_start: 0.4837 (t80) cc_final: 0.4434 (t80) REVERT: K 250 ILE cc_start: 0.7799 (mm) cc_final: 0.7450 (pt) REVERT: K 315 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7639 (mtmt) REVERT: N 204 LYS cc_start: 0.4011 (mttt) cc_final: 0.3627 (ptpt) REVERT: N 269 SER cc_start: 0.8083 (t) cc_final: 0.7847 (p) REVERT: N 271 ASP cc_start: 0.7107 (p0) cc_final: 0.6545 (t0) REVERT: N 275 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: N 339 LEU cc_start: 0.4706 (tt) cc_final: 0.4054 (mt) outliers start: 91 outliers final: 67 residues processed: 463 average time/residue: 0.2102 time to fit residues: 160.8146 Evaluate side-chains 460 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 383 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 438 TYR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1310 GLN Chi-restraints excluded: chain H residue 1323 SER Chi-restraints excluded: chain H residue 1382 LEU Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain H residue 2186 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 250 TRP Chi-restraints excluded: chain J residue 302 LEU Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 441 CYS Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 471 HIS Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain N residue 275 GLU Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 297 optimal weight: 20.0000 chunk 431 optimal weight: 0.7980 chunk 253 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 305 optimal weight: 10.0000 chunk 123 optimal weight: 0.6980 chunk 326 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 467 optimal weight: 0.5980 chunk 32 optimal weight: 0.2980 chunk 365 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN C 115 ASN D 226 GLN D 344 HIS ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 176 HIS M 416 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.170830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.131433 restraints weight = 58064.493| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.16 r_work: 0.3289 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 39679 Z= 0.107 Angle : 0.576 11.274 53595 Z= 0.277 Chirality : 0.042 0.233 6084 Planarity : 0.004 0.059 6846 Dihedral : 5.373 143.732 5450 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.13 % Allowed : 13.96 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.12), residues: 4848 helix: 1.38 (0.12), residues: 2039 sheet: -0.58 (0.19), residues: 722 loop : -1.03 (0.14), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 248 TYR 0.029 0.001 TYR G 246 PHE 0.016 0.001 PHE I 262 TRP 0.023 0.001 TRP I 394 HIS 0.009 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00241 (39668) covalent geometry : angle 0.57566 (53595) hydrogen bonds : bond 0.02964 ( 1642) hydrogen bonds : angle 4.09227 ( 4629) Misc. bond : bond 0.00150 ( 11) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 396 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8889 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: A 259 MET cc_start: 0.6549 (pmm) cc_final: 0.6226 (pmm) REVERT: B 90 MET cc_start: 0.8704 (ttm) cc_final: 0.8376 (mtp) REVERT: B 116 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 169 GLU cc_start: 0.5857 (mt-10) cc_final: 0.5060 (tm-30) REVERT: B 267 GLU cc_start: 0.5705 (pt0) cc_final: 0.4941 (mm-30) REVERT: B 354 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8992 (pp) REVERT: C 244 ASP cc_start: 0.8285 (m-30) cc_final: 0.7880 (m-30) REVERT: C 249 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7558 (ttm-80) REVERT: C 270 GLU cc_start: 0.7026 (mp0) cc_final: 0.6752 (mp0) REVERT: C 274 LYS cc_start: 0.8939 (ttpp) cc_final: 0.8550 (ttpp) REVERT: C 308 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7624 (t0) REVERT: C 374 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8527 (mt) REVERT: D 29 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7470 (mtt-85) REVERT: D 180 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7494 (mm-30) REVERT: E 61 MET cc_start: 0.9128 (mmm) cc_final: 0.8760 (mmm) REVERT: E 237 ASP cc_start: 0.7938 (p0) cc_final: 0.7664 (p0) REVERT: E 260 MET cc_start: 0.3841 (ttt) cc_final: 0.3076 (ttt) REVERT: F 132 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7904 (pttt) REVERT: F 136 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7283 (mm-30) REVERT: F 269 LYS cc_start: 0.8247 (tppt) cc_final: 0.7757 (ttmt) REVERT: F 376 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8224 (tt0) REVERT: G 58 TYR cc_start: 0.4738 (m-80) cc_final: 0.4458 (m-80) REVERT: G 60 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.5957 (mp) REVERT: G 231 GLU cc_start: 0.7010 (pt0) cc_final: 0.6447 (tm-30) REVERT: G 261 ARG cc_start: 0.6309 (ttt-90) cc_final: 0.6038 (mpt180) REVERT: H 830 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7632 (tm) REVERT: H 845 TRP cc_start: 0.4921 (m100) cc_final: 0.3602 (t60) REVERT: H 1118 LYS cc_start: 0.4347 (mttt) cc_final: 0.3789 (tppt) REVERT: H 1185 MET cc_start: 0.1747 (mmp) cc_final: 0.1315 (tmm) REVERT: H 1225 MET cc_start: 0.3340 (tpp) cc_final: 0.2801 (tpp) REVERT: H 1310 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: H 1327 ARG cc_start: 0.5795 (mtp180) cc_final: 0.5304 (mtt180) REVERT: H 1877 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6716 (mp0) REVERT: H 1890 MET cc_start: 0.8760 (tpt) cc_final: 0.8330 (tpt) REVERT: H 2177 LEU cc_start: 0.7750 (tp) cc_final: 0.7499 (tp) REVERT: H 2193 TYR cc_start: 0.6460 (t80) cc_final: 0.5856 (t80) REVERT: I 152 CYS cc_start: 0.7128 (p) cc_final: 0.6802 (p) REVERT: I 213 MET cc_start: 0.0961 (mpt) cc_final: 0.0538 (mmt) REVERT: I 272 SER cc_start: 0.4329 (m) cc_final: 0.3888 (p) REVERT: J 82 MET cc_start: 0.6087 (ttt) cc_final: 0.5157 (ttm) REVERT: J 130 ARG cc_start: 0.7705 (ttt-90) cc_final: 0.7362 (mtp-110) REVERT: J 243 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7328 (tt) REVERT: J 335 MET cc_start: 0.7066 (mtp) cc_final: 0.6648 (mtt) REVERT: J 348 VAL cc_start: 0.8015 (t) cc_final: 0.7748 (p) REVERT: K 188 TYR cc_start: 0.7037 (t80) cc_final: 0.6751 (t80) REVERT: K 208 ILE cc_start: 0.8012 (mp) cc_final: 0.7753 (mt) REVERT: K 240 TYR cc_start: 0.4827 (t80) cc_final: 0.4406 (t80) REVERT: K 250 ILE cc_start: 0.7722 (mm) cc_final: 0.7335 (pt) REVERT: K 315 LYS cc_start: 0.7910 (ttmm) cc_final: 0.7599 (mtmt) REVERT: M 404 PHE cc_start: 0.5592 (t80) cc_final: 0.5167 (t80) REVERT: M 518 LEU cc_start: 0.3408 (OUTLIER) cc_final: 0.2744 (mm) REVERT: N 204 LYS cc_start: 0.4022 (mttt) cc_final: 0.3633 (ptpt) REVERT: N 269 SER cc_start: 0.8301 (t) cc_final: 0.7994 (p) REVERT: N 271 ASP cc_start: 0.7119 (p0) cc_final: 0.5990 (p0) REVERT: N 275 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6497 (mp0) REVERT: N 339 LEU cc_start: 0.4885 (tt) cc_final: 0.4131 (mt) outliers start: 90 outliers final: 67 residues processed: 458 average time/residue: 0.2048 time to fit residues: 155.7208 Evaluate side-chains 460 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 381 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 438 TYR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 825 GLU Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 836 SER Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1310 GLN Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1743 SER Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain H residue 2186 THR Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 221 TYR Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 250 TRP Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 441 CYS Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 471 HIS Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 275 GLU Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 132 optimal weight: 0.9990 chunk 283 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 464 optimal weight: 10.0000 chunk 316 optimal weight: 0.2980 chunk 172 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN D 226 GLN I 128 ASN I 313 ASN J 327 HIS K 12 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130912 restraints weight = 58348.794| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.11 r_work: 0.3278 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39679 Z= 0.121 Angle : 0.588 11.397 53595 Z= 0.284 Chirality : 0.043 0.256 6084 Planarity : 0.004 0.059 6846 Dihedral : 5.405 143.219 5450 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.11 % Allowed : 14.08 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.12), residues: 4848 helix: 1.40 (0.12), residues: 2032 sheet: -0.54 (0.19), residues: 741 loop : -1.02 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H1783 TYR 0.023 0.001 TYR G 246 PHE 0.018 0.001 PHE B 257 TRP 0.025 0.001 TRP I 394 HIS 0.009 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00280 (39668) covalent geometry : angle 0.58797 (53595) hydrogen bonds : bond 0.03113 ( 1642) hydrogen bonds : angle 4.10566 ( 4629) Misc. bond : bond 0.00180 ( 11) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 388 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: A 259 MET cc_start: 0.6534 (pmm) cc_final: 0.6235 (pmm) REVERT: B 90 MET cc_start: 0.8709 (ttm) cc_final: 0.8405 (mtp) REVERT: B 116 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8714 (p) REVERT: B 267 GLU cc_start: 0.5845 (pt0) cc_final: 0.5117 (mm-30) REVERT: B 354 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.8977 (pp) REVERT: C 244 ASP cc_start: 0.8304 (m-30) cc_final: 0.7893 (m-30) REVERT: C 249 ARG cc_start: 0.7977 (ptm160) cc_final: 0.7612 (ttm110) REVERT: C 274 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8585 (ttpp) REVERT: C 308 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7627 (t0) REVERT: C 374 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8587 (mt) REVERT: D 29 ARG cc_start: 0.7732 (ttm110) cc_final: 0.7485 (mtt-85) REVERT: D 180 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7638 (mm-30) REVERT: E 61 MET cc_start: 0.9124 (mmm) cc_final: 0.8745 (mmm) REVERT: E 237 ASP cc_start: 0.7973 (p0) cc_final: 0.7669 (p0) REVERT: E 260 MET cc_start: 0.3856 (ttt) cc_final: 0.3297 (ttt) REVERT: F 132 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7907 (pttt) REVERT: F 136 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7281 (mm-30) REVERT: F 269 LYS cc_start: 0.8267 (tppt) cc_final: 0.7788 (ttmt) REVERT: F 376 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8197 (tt0) REVERT: G 60 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.5924 (mp) REVERT: G 231 GLU cc_start: 0.6849 (pt0) cc_final: 0.6318 (tm-30) REVERT: G 261 ARG cc_start: 0.6294 (ttt-90) cc_final: 0.6028 (mpt180) REVERT: H 830 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7711 (tm) REVERT: H 845 TRP cc_start: 0.4986 (m100) cc_final: 0.3640 (t60) REVERT: H 1118 LYS cc_start: 0.4352 (mttt) cc_final: 0.3786 (tppt) REVERT: H 1185 MET cc_start: 0.1870 (mmp) cc_final: 0.1284 (tmm) REVERT: H 1191 MET cc_start: 0.3002 (mtm) cc_final: 0.1834 (pmm) REVERT: H 1225 MET cc_start: 0.3012 (tpp) cc_final: 0.2505 (tpp) REVERT: H 1327 ARG cc_start: 0.5476 (mtp180) cc_final: 0.4949 (mtt180) REVERT: H 1397 LYS cc_start: 0.6588 (mmmt) cc_final: 0.5962 (tptt) REVERT: H 1890 MET cc_start: 0.8872 (tpt) cc_final: 0.8457 (tpt) REVERT: H 2177 LEU cc_start: 0.7858 (tp) cc_final: 0.7628 (tp) REVERT: H 2193 TYR cc_start: 0.6272 (t80) cc_final: 0.5664 (t80) REVERT: I 213 MET cc_start: 0.0758 (mpt) cc_final: 0.0313 (mmt) REVERT: I 272 SER cc_start: 0.4319 (m) cc_final: 0.3871 (p) REVERT: J 82 MET cc_start: 0.5998 (ttt) cc_final: 0.5792 (ttm) REVERT: J 130 ARG cc_start: 0.7709 (ttt-90) cc_final: 0.7396 (mtp-110) REVERT: J 243 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7337 (tt) REVERT: J 335 MET cc_start: 0.7057 (mtp) cc_final: 0.6648 (mtt) REVERT: J 348 VAL cc_start: 0.7998 (t) cc_final: 0.7757 (p) REVERT: K 250 ILE cc_start: 0.7793 (mm) cc_final: 0.7272 (pt) REVERT: K 315 LYS cc_start: 0.7901 (ttmm) cc_final: 0.7588 (mtmt) REVERT: M 404 PHE cc_start: 0.5630 (t80) cc_final: 0.5209 (t80) REVERT: M 518 LEU cc_start: 0.3453 (OUTLIER) cc_final: 0.2755 (mm) REVERT: N 204 LYS cc_start: 0.4016 (mttt) cc_final: 0.3629 (ptpt) REVERT: N 269 SER cc_start: 0.8249 (t) cc_final: 0.8003 (p) REVERT: N 271 ASP cc_start: 0.7205 (p0) cc_final: 0.6089 (p0) REVERT: N 275 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6444 (mp0) REVERT: N 339 LEU cc_start: 0.4562 (tt) cc_final: 0.3979 (mt) outliers start: 89 outliers final: 71 residues processed: 450 average time/residue: 0.2101 time to fit residues: 157.8685 Evaluate side-chains 456 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 374 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 259 MET Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 825 GLU Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 836 SER Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1310 GLN Chi-restraints excluded: chain H residue 1382 LEU Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1743 SER Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain H residue 2230 MET Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 250 TRP Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 441 CYS Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 471 HIS Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 275 GLU Chi-restraints excluded: chain N residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 431 optimal weight: 7.9990 chunk 378 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 442 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 206 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 385 optimal weight: 0.9980 chunk 462 optimal weight: 20.0000 chunk 177 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN D 226 GLN H1839 GLN K 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.170076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131159 restraints weight = 57916.711| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.23 r_work: 0.3311 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39679 Z= 0.112 Angle : 0.581 11.929 53595 Z= 0.279 Chirality : 0.042 0.253 6084 Planarity : 0.004 0.060 6846 Dihedral : 5.349 140.652 5450 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.99 % Allowed : 14.25 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.12), residues: 4848 helix: 1.48 (0.12), residues: 2021 sheet: -0.54 (0.19), residues: 746 loop : -0.99 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H1783 TYR 0.021 0.001 TYR G 246 PHE 0.017 0.001 PHE J 262 TRP 0.037 0.001 TRP I 394 HIS 0.009 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00255 (39668) covalent geometry : angle 0.58081 (53595) hydrogen bonds : bond 0.02989 ( 1642) hydrogen bonds : angle 4.06925 ( 4629) Misc. bond : bond 0.00156 ( 11) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 390 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: A 259 MET cc_start: 0.6365 (pmm) cc_final: 0.6111 (pmm) REVERT: B 90 MET cc_start: 0.8634 (ttm) cc_final: 0.8378 (mtp) REVERT: B 116 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 267 GLU cc_start: 0.5800 (pt0) cc_final: 0.5090 (mm-30) REVERT: B 354 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8975 (pp) REVERT: C 244 ASP cc_start: 0.8251 (m-30) cc_final: 0.7802 (m-30) REVERT: C 249 ARG cc_start: 0.8010 (ptm160) cc_final: 0.7676 (ttm-80) REVERT: C 274 LYS cc_start: 0.8940 (ttpp) cc_final: 0.8547 (ttpp) REVERT: C 308 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7488 (t0) REVERT: C 374 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8592 (mt) REVERT: D 180 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7664 (mm-30) REVERT: E 61 MET cc_start: 0.9111 (mmm) cc_final: 0.8743 (mmm) REVERT: E 237 ASP cc_start: 0.7921 (p0) cc_final: 0.7595 (p0) REVERT: E 260 MET cc_start: 0.3548 (ttt) cc_final: 0.3012 (ttt) REVERT: F 132 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7875 (pttt) REVERT: F 136 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7268 (mm-30) REVERT: F 269 LYS cc_start: 0.8192 (tppt) cc_final: 0.7773 (ttmt) REVERT: F 376 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8148 (tt0) REVERT: G 60 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6078 (mp) REVERT: G 261 ARG cc_start: 0.6343 (ttt-90) cc_final: 0.6057 (mpt180) REVERT: H 830 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7673 (tm) REVERT: H 845 TRP cc_start: 0.4985 (m100) cc_final: 0.3616 (t60) REVERT: H 1118 LYS cc_start: 0.4345 (mttt) cc_final: 0.3811 (tppt) REVERT: H 1185 MET cc_start: 0.1201 (mmp) cc_final: 0.0665 (tmm) REVERT: H 1191 MET cc_start: 0.3057 (mtm) cc_final: 0.1888 (pmm) REVERT: H 1225 MET cc_start: 0.2974 (tpp) cc_final: 0.2480 (tpp) REVERT: H 1327 ARG cc_start: 0.5556 (mtp180) cc_final: 0.5054 (mtt180) REVERT: H 1890 MET cc_start: 0.8837 (tpt) cc_final: 0.8413 (tpt) REVERT: H 2177 LEU cc_start: 0.7864 (tp) cc_final: 0.7637 (tp) REVERT: H 2193 TYR cc_start: 0.6452 (t80) cc_final: 0.5830 (t80) REVERT: I 213 MET cc_start: 0.0760 (mpt) cc_final: 0.0266 (mtt) REVERT: I 272 SER cc_start: 0.4259 (m) cc_final: 0.3831 (p) REVERT: I 282 MET cc_start: 0.2775 (ppp) cc_final: 0.2393 (ptm) REVERT: I 335 MET cc_start: 0.1619 (ptt) cc_final: 0.1143 (ptm) REVERT: J 82 MET cc_start: 0.5895 (ttt) cc_final: 0.5034 (ttm) REVERT: J 109 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7716 (mmt) REVERT: J 130 ARG cc_start: 0.7685 (ttt-90) cc_final: 0.7376 (mtp-110) REVERT: J 206 CYS cc_start: 0.6370 (m) cc_final: 0.5994 (m) REVERT: J 243 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7351 (tt) REVERT: J 335 MET cc_start: 0.6979 (mtp) cc_final: 0.6588 (mtt) REVERT: J 348 VAL cc_start: 0.8032 (t) cc_final: 0.7789 (p) REVERT: K 188 TYR cc_start: 0.7037 (t80) cc_final: 0.6590 (t80) REVERT: K 240 TYR cc_start: 0.4901 (t80) cc_final: 0.4515 (t80) REVERT: K 250 ILE cc_start: 0.7760 (mm) cc_final: 0.7246 (pt) REVERT: K 315 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7568 (mtmt) REVERT: M 404 PHE cc_start: 0.5650 (t80) cc_final: 0.5247 (t80) REVERT: M 518 LEU cc_start: 0.3398 (OUTLIER) cc_final: 0.2698 (mm) REVERT: N 204 LYS cc_start: 0.3897 (mttt) cc_final: 0.3601 (ptpt) REVERT: N 269 SER cc_start: 0.8288 (t) cc_final: 0.8050 (p) REVERT: N 271 ASP cc_start: 0.7305 (p0) cc_final: 0.6241 (p0) REVERT: N 275 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: N 339 LEU cc_start: 0.4825 (tt) cc_final: 0.4126 (tp) outliers start: 84 outliers final: 67 residues processed: 449 average time/residue: 0.2089 time to fit residues: 156.2016 Evaluate side-chains 460 residues out of total 4219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 381 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 413 CYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 308 ASP Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 396 GLU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 446 TYR Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 385 ASN Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 251 ASN Chi-restraints excluded: chain F residue 338 THR Chi-restraints excluded: chain F residue 398 SER Chi-restraints excluded: chain F residue 413 CYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 234 TYR Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain H residue 825 GLU Chi-restraints excluded: chain H residue 830 LEU Chi-restraints excluded: chain H residue 836 SER Chi-restraints excluded: chain H residue 1188 VAL Chi-restraints excluded: chain H residue 1310 GLN Chi-restraints excluded: chain H residue 1382 LEU Chi-restraints excluded: chain H residue 1389 HIS Chi-restraints excluded: chain H residue 1743 SER Chi-restraints excluded: chain H residue 1749 TRP Chi-restraints excluded: chain H residue 1811 VAL Chi-restraints excluded: chain I residue 23 VAL Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 328 VAL Chi-restraints excluded: chain I residue 403 LEU Chi-restraints excluded: chain J residue 23 VAL Chi-restraints excluded: chain J residue 109 MET Chi-restraints excluded: chain J residue 243 LEU Chi-restraints excluded: chain J residue 250 TRP Chi-restraints excluded: chain J residue 325 VAL Chi-restraints excluded: chain J residue 386 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain K residue 293 LEU Chi-restraints excluded: chain M residue 441 CYS Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 471 HIS Chi-restraints excluded: chain M residue 479 HIS Chi-restraints excluded: chain M residue 518 LEU Chi-restraints excluded: chain N residue 211 ILE Chi-restraints excluded: chain N residue 275 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 442 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 56 optimal weight: 0.0370 chunk 356 optimal weight: 3.9990 chunk 321 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 chunk 392 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 342 optimal weight: 9.9990 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN C 115 ASN D 226 GLN D 447 GLN ** E 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 747 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.168751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129515 restraints weight = 58027.174| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.27 r_work: 0.3281 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39679 Z= 0.128 Angle : 0.597 12.501 53595 Z= 0.288 Chirality : 0.043 0.258 6084 Planarity : 0.004 0.059 6846 Dihedral : 5.444 142.078 5450 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.01 % Allowed : 14.22 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.12), residues: 4848 helix: 1.38 (0.12), residues: 2040 sheet: -0.50 (0.19), residues: 741 loop : -1.00 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 333 TYR 0.020 0.001 TYR G 246 PHE 0.017 0.001 PHE J 262 TRP 0.031 0.001 TRP I 394 HIS 0.010 0.001 HIS E 316 Details of bonding type rmsd covalent geometry : bond 0.00300 (39668) covalent geometry : angle 0.59687 (53595) hydrogen bonds : bond 0.03181 ( 1642) hydrogen bonds : angle 4.12535 ( 4629) Misc. bond : bond 0.00191 ( 11) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9328.07 seconds wall clock time: 160 minutes 29.28 seconds (9629.28 seconds total)