Starting phenix.real_space_refine on Fri Feb 16 20:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpv_22989/02_2024/7kpv_22989.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpv_22989/02_2024/7kpv_22989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpv_22989/02_2024/7kpv_22989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpv_22989/02_2024/7kpv_22989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpv_22989/02_2024/7kpv_22989.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kpv_22989/02_2024/7kpv_22989.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 10658 2.51 5 N 2771 2.21 5 O 2943 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 212": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 486": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ARG 318": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C GLU 1381": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D ARG 898": "NH1" <-> "NH2" Residue "D ARG 1077": "NH1" <-> "NH2" Residue "D ARG 1118": "NH1" <-> "NH2" Residue "D ARG 1158": "NH1" <-> "NH2" Residue "D GLU 1163": "OE1" <-> "OE2" Residue "D ARG 1219": "NH1" <-> "NH2" Residue "D ARG 1234": "NH1" <-> "NH2" Residue "D ARG 1238": "NH1" <-> "NH2" Residue "D PHE 1255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1374": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16449 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2952 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 17, 'TRANS': 339} Chain breaks: 3 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2436 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 15, 'TRANS': 274} Chain breaks: 2 Chain: "C" Number of atoms: 4049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 4049 Classifications: {'peptide': 487} Link IDs: {'PTRANS': 19, 'TRANS': 467} Chain breaks: 2 Chain: "D" Number of atoms: 7012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 876, 7012 Classifications: {'peptide': 876} Link IDs: {'PTRANS': 51, 'TRANS': 824} Chain breaks: 2 Time building chain proxies: 8.49, per 1000 atoms: 0.52 Number of scatterers: 16449 At special positions: 0 Unit cell: (123.05, 146.59, 155.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 2943 8.00 N 2771 7.00 C 10658 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.6 seconds 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 40.7% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 57 through 66 removed outlier: 3.758A pdb=" N ALA A 62 " --> pdb=" O GLY A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.898A pdb=" N GLU A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.733A pdb=" N ASN A 280 " --> pdb=" O TYR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 331 removed outlier: 3.955A pdb=" N ARG A 331 " --> pdb=" O ILE A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 383 through 393 Processing helix chain 'A' and resid 402 through 406 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 421 through 428 Processing helix chain 'A' and resid 435 through 444 removed outlier: 3.702A pdb=" N LEU A 439 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 34 removed outlier: 4.556A pdb=" N GLN B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 Processing helix chain 'B' and resid 92 through 110 removed outlier: 3.728A pdb=" N LEU B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 Processing helix chain 'B' and resid 137 through 149 Processing helix chain 'B' and resid 156 through 171 removed outlier: 4.108A pdb=" N VAL B 160 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 removed outlier: 4.032A pdb=" N SER B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 225 through 243 removed outlier: 3.744A pdb=" N ILE B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 279 Processing helix chain 'B' and resid 285 through 300 Processing helix chain 'B' and resid 304 through 317 removed outlier: 4.236A pdb=" N ILE B 308 " --> pdb=" O HIS B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 49 removed outlier: 3.833A pdb=" N ASP C 43 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 97 Processing helix chain 'C' and resid 122 through 134 removed outlier: 3.623A pdb=" N HIS C 131 " --> pdb=" O GLU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 166 through 188 Processing helix chain 'C' and resid 198 through 225 removed outlier: 4.105A pdb=" N MET C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N THR C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 252 removed outlier: 3.917A pdb=" N ARG C 238 " --> pdb=" O ARG C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 272 removed outlier: 3.520A pdb=" N HIS C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N HIS C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 277 through 288 removed outlier: 3.606A pdb=" N HIS C 283 " --> pdb=" O PRO C 279 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE C 288 " --> pdb=" O ILE C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.674A pdb=" N CYS C 293 " --> pdb=" O TRP C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 333 removed outlier: 3.800A pdb=" N THR C 317 " --> pdb=" O PHE C 313 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER C 333 " --> pdb=" O ILE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 372 removed outlier: 3.616A pdb=" N ASN C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 399 through 413 Processing helix chain 'C' and resid 1413 through 1417 Processing helix chain 'D' and resid 33 through 37 removed outlier: 4.050A pdb=" N GLN D 36 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 33 through 37' Processing helix chain 'D' and resid 39 through 50 removed outlier: 3.971A pdb=" N PHE D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 125 removed outlier: 3.952A pdb=" N LYS D 111 " --> pdb=" O ALA D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 179 through 184 Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.681A pdb=" N THR D 220 " --> pdb=" O GLU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 249 Processing helix chain 'D' and resid 296 through 311 removed outlier: 3.845A pdb=" N ALA D 300 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 822 removed outlier: 3.658A pdb=" N ARG D 822 " --> pdb=" O PRO D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 859 removed outlier: 4.133A pdb=" N THR D 859 " --> pdb=" O GLU D 855 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 893 Processing helix chain 'D' and resid 900 through 904 removed outlier: 3.955A pdb=" N THR D 904 " --> pdb=" O ASN D 900 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 900 through 904' Processing helix chain 'D' and resid 958 through 975 removed outlier: 3.649A pdb=" N CYS D 962 " --> pdb=" O PHE D 958 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER D 964 " --> pdb=" O GLU D 960 " (cutoff:3.500A) Proline residue: D 967 - end of helix Processing helix chain 'D' and resid 1001 through 1019 Processing helix chain 'D' and resid 1042 through 1059 removed outlier: 3.607A pdb=" N ALA D1059 " --> pdb=" O ASN D1055 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1078 Processing helix chain 'D' and resid 1085 through 1095 removed outlier: 3.679A pdb=" N VAL D1089 " --> pdb=" O GLN D1085 " (cutoff:3.500A) Processing helix chain 'D' and resid 1188 through 1207 removed outlier: 3.876A pdb=" N ASP D1192 " --> pdb=" O ARG D1188 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TRP D1199 " --> pdb=" O CYS D1195 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1236 removed outlier: 3.587A pdb=" N LEU D1229 " --> pdb=" O PRO D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1265 through 1271 removed outlier: 4.055A pdb=" N ASP D1271 " --> pdb=" O PRO D1267 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1364 removed outlier: 3.622A pdb=" N LEU D1350 " --> pdb=" O ASP D1346 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN D1360 " --> pdb=" O GLU D1356 " (cutoff:3.500A) Processing helix chain 'D' and resid 1365 through 1367 No H-bonds generated for 'chain 'D' and resid 1365 through 1367' Processing helix chain 'D' and resid 1379 through 1392 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 81 removed outlier: 6.803A pdb=" N LYS A 91 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N TYR A 80 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N VAL A 89 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 88 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 180 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 224 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119 removed outlier: 3.596A pdb=" N ILE C 119 " --> pdb=" O ILE C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 1373 through 1377 removed outlier: 6.838A pdb=" N ILE C1366 " --> pdb=" O VAL C1375 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C1377 " --> pdb=" O TRP C1364 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N TRP C1364 " --> pdb=" O THR C1377 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C1365 " --> pdb=" O ARG D1289 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU D1287 " --> pdb=" O TYR C1367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 153 Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 59 removed outlier: 4.626A pdb=" N LEU D 56 " --> pdb=" O PHE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 129 through 131 Processing sheet with id=AA8, first strand: chain 'D' and resid 171 through 172 removed outlier: 11.998A pdb=" N HIS D 186 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N LEU D 199 " --> pdb=" O HIS D 186 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU D 188 " --> pdb=" O MET D 197 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 839 through 842 Processing sheet with id=AB1, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER D1150 " --> pdb=" O CYS D1214 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ILE D1216 " --> pdb=" O SER D1150 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D1152 " --> pdb=" O ILE D1216 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR D1218 " --> pdb=" O ILE D1152 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU D1154 " --> pdb=" O THR D1218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 905 through 910 removed outlier: 5.294A pdb=" N SER D1317 " --> pdb=" O PHE D1300 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ARG D1316 " --> pdb=" O LEU D1339 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU D1339 " --> pdb=" O ARG D1316 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL D1244 " --> pdb=" O LEU D1340 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE D1213 " --> pdb=" O HIS D1241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 915 through 919 Processing sheet with id=AB4, first strand: chain 'D' and resid 950 through 953 removed outlier: 6.659A pdb=" N LYS D 950 " --> pdb=" O LEU D1030 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE D1032 " --> pdb=" O LYS D 950 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 952 " --> pdb=" O ILE D1032 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE D1029 " --> pdb=" O TYR D1067 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LYS D1069 " --> pdb=" O ILE D1029 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE D1031 " --> pdb=" O LYS D1069 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ILE D1071 " --> pdb=" O ILE D1031 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU D1033 " --> pdb=" O ILE D1071 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 1256 through 1257 648 hydrogen bonds defined for protein. 1869 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: 5.36 Time building geometry restraints manager: 6.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4590 1.34 - 1.45: 2939 1.45 - 1.57: 9224 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16873 Sorted by residual: bond pdb=" CA PRO D1027 " pdb=" C PRO D1027 " ideal model delta sigma weight residual 1.517 1.547 -0.030 9.30e-03 1.16e+04 1.04e+01 bond pdb=" N GLU C 311 " pdb=" CA GLU C 311 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.04e+00 bond pdb=" CA HIS B 63 " pdb=" C HIS B 63 " ideal model delta sigma weight residual 1.528 1.566 -0.038 1.37e-02 5.33e+03 7.73e+00 bond pdb=" N LYS C 310 " pdb=" CA LYS C 310 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.22e-02 6.72e+03 6.61e+00 bond pdb=" N ILE C 343 " pdb=" CA ILE C 343 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.25e-02 6.40e+03 3.93e+00 ... (remaining 16868 not shown) Histogram of bond angle deviations from ideal: 99.23 - 106.72: 583 106.72 - 114.20: 9780 114.20 - 121.69: 8762 121.69 - 129.17: 3583 129.17 - 136.66: 169 Bond angle restraints: 22877 Sorted by residual: angle pdb=" N PRO D1027 " pdb=" CA PRO D1027 " pdb=" C PRO D1027 " ideal model delta sigma weight residual 110.70 123.97 -13.27 1.22e+00 6.72e-01 1.18e+02 angle pdb=" C PRO D1027 " pdb=" N PRO D1028 " pdb=" CA PRO D1028 " ideal model delta sigma weight residual 119.76 109.94 9.82 1.03e+00 9.43e-01 9.10e+01 angle pdb=" N HIS B 63 " pdb=" CA HIS B 63 " pdb=" C HIS B 63 " ideal model delta sigma weight residual 110.53 102.80 7.73 1.29e+00 6.01e-01 3.59e+01 angle pdb=" N TYR C 342 " pdb=" CA TYR C 342 " pdb=" C TYR C 342 " ideal model delta sigma weight residual 110.41 116.85 -6.44 1.23e+00 6.61e-01 2.75e+01 angle pdb=" C PRO A 379 " pdb=" N PHE A 380 " pdb=" CA PHE A 380 " ideal model delta sigma weight residual 121.54 131.24 -9.70 1.91e+00 2.74e-01 2.58e+01 ... (remaining 22872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8809 17.94 - 35.88: 901 35.88 - 53.83: 331 53.83 - 71.77: 90 71.77 - 89.71: 13 Dihedral angle restraints: 10144 sinusoidal: 4172 harmonic: 5972 Sorted by residual: dihedral pdb=" CA LEU D 59 " pdb=" C LEU D 59 " pdb=" N LEU D 60 " pdb=" CA LEU D 60 " ideal model delta harmonic sigma weight residual 180.00 151.79 28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ASP D 12 " pdb=" C ASP D 12 " pdb=" N VAL D 13 " pdb=" CA VAL D 13 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA HIS A 196 " pdb=" C HIS A 196 " pdb=" N TYR A 197 " pdb=" CA TYR A 197 " ideal model delta harmonic sigma weight residual 180.00 153.45 26.55 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 10141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2021 0.064 - 0.128: 466 0.128 - 0.192: 50 0.192 - 0.256: 7 0.256 - 0.320: 4 Chirality restraints: 2548 Sorted by residual: chirality pdb=" CA PRO D1027 " pdb=" N PRO D1027 " pdb=" C PRO D1027 " pdb=" CB PRO D1027 " both_signs ideal model delta sigma weight residual False 2.72 2.40 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA THR C 11 " pdb=" N THR C 11 " pdb=" C THR C 11 " pdb=" CB THR C 11 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA PHE C 313 " pdb=" N PHE C 313 " pdb=" C PHE C 313 " pdb=" CB PHE C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 2545 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 340 " -0.020 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C GLU C 340 " 0.070 2.00e-02 2.50e+03 pdb=" O GLU C 340 " -0.027 2.00e-02 2.50e+03 pdb=" N ASN C 341 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 343 " -0.054 5.00e-02 4.00e+02 8.15e-02 1.06e+01 pdb=" N PRO A 344 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 344 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 344 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D1098 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO D1099 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D1099 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D1099 " 0.045 5.00e-02 4.00e+02 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1203 2.73 - 3.28: 15481 3.28 - 3.82: 26243 3.82 - 4.36: 28923 4.36 - 4.90: 50711 Nonbonded interactions: 122561 Sorted by model distance: nonbonded pdb=" N ASP B 65 " pdb=" OD1 ASP B 65 " model vdw 2.193 2.520 nonbonded pdb=" O LEU B 66 " pdb=" ND1 HIS B 67 " model vdw 2.270 2.520 nonbonded pdb=" O ILE B 217 " pdb=" ND2 ASN B 218 " model vdw 2.274 2.520 nonbonded pdb=" OG SER D1159 " pdb=" OD1 ASP D1161 " model vdw 2.287 2.440 nonbonded pdb=" OG SER D1159 " pdb=" O ASP D1161 " model vdw 2.299 2.440 ... (remaining 122556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.780 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 41.840 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16873 Z= 0.307 Angle : 0.901 13.272 22877 Z= 0.512 Chirality : 0.054 0.320 2548 Planarity : 0.007 0.082 2871 Dihedral : 17.415 89.712 6262 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 17.46 % Allowed : 13.72 % Favored : 68.82 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.15), residues: 1984 helix: -2.35 (0.14), residues: 750 sheet: -2.28 (0.32), residues: 211 loop : -3.56 (0.16), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 14 HIS 0.010 0.001 HIS A 341 PHE 0.023 0.002 PHE D 294 TYR 0.026 0.002 TYR C 178 ARG 0.004 0.000 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 378 time to evaluate : 1.968 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: A 52 ASN cc_start: 0.7101 (p0) cc_final: 0.6748 (t0) REVERT: A 182 ILE cc_start: 0.8629 (mt) cc_final: 0.8356 (mt) REVERT: A 198 THR cc_start: 0.5579 (m) cc_final: 0.5136 (p) REVERT: A 230 LYS cc_start: 0.7856 (mmtt) cc_final: 0.7590 (mttt) REVERT: A 256 ARG cc_start: 0.5077 (mtt180) cc_final: 0.3440 (mmm160) REVERT: A 314 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8341 (ptp) REVERT: A 349 TRP cc_start: 0.8089 (t-100) cc_final: 0.7864 (t-100) REVERT: A 398 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5526 (tmtt) REVERT: A 408 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6199 (pm20) REVERT: A 434 LYS cc_start: 0.6944 (mtmm) cc_final: 0.6598 (tptt) REVERT: A 446 TYR cc_start: 0.7605 (OUTLIER) cc_final: 0.5243 (p90) REVERT: A 465 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: A 486 ARG cc_start: 0.6968 (tpt90) cc_final: 0.5684 (mtp-110) REVERT: B 24 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7082 (tm-30) REVERT: B 33 CYS cc_start: 0.7472 (t) cc_final: 0.7186 (m) REVERT: B 40 LEU cc_start: 0.7877 (tp) cc_final: 0.7229 (tp) REVERT: B 45 ASP cc_start: 0.3413 (OUTLIER) cc_final: 0.3198 (m-30) REVERT: B 63 HIS cc_start: 0.5962 (OUTLIER) cc_final: 0.5682 (m90) REVERT: B 65 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7137 (p0) REVERT: B 83 MET cc_start: 0.7663 (tpp) cc_final: 0.7281 (ttm) REVERT: B 90 ASN cc_start: 0.5176 (t0) cc_final: 0.4922 (t0) REVERT: B 166 TYR cc_start: 0.8445 (m-80) cc_final: 0.8122 (m-10) REVERT: B 185 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: C 85 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8013 (mp-120) REVERT: C 95 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7825 (m-30) REVERT: C 159 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6440 (mm-40) REVERT: C 294 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: C 343 ILE cc_start: 0.5460 (OUTLIER) cc_final: 0.5253 (pt) REVERT: C 353 ILE cc_start: 0.8402 (mt) cc_final: 0.7825 (pt) REVERT: C 361 LEU cc_start: 0.8990 (mt) cc_final: 0.8744 (mp) REVERT: C 371 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: C 1392 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7326 (mtpt) REVERT: C 1423 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7276 (ptt-90) REVERT: D 24 LYS cc_start: 0.8240 (pttp) cc_final: 0.7674 (mttt) REVERT: D 25 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7791 (tttt) REVERT: D 34 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6623 (pttt) REVERT: D 38 ASP cc_start: 0.5591 (OUTLIER) cc_final: 0.5320 (m-30) REVERT: D 144 ASN cc_start: 0.8248 (t0) cc_final: 0.8026 (t0) REVERT: D 197 MET cc_start: 0.7582 (ppp) cc_final: 0.7229 (ppp) REVERT: D 296 CYS cc_start: 0.7418 (t) cc_final: 0.6839 (m) REVERT: D 298 GLN cc_start: 0.7621 (tp40) cc_final: 0.6603 (mm-40) REVERT: D 305 ASP cc_start: 0.6267 (OUTLIER) cc_final: 0.5637 (t70) REVERT: D 855 GLU cc_start: 0.7741 (tt0) cc_final: 0.7538 (tt0) REVERT: D 860 ASP cc_start: 0.7937 (t0) cc_final: 0.7563 (t0) REVERT: D 863 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8296 (pt) REVERT: D 916 VAL cc_start: 0.9125 (OUTLIER) cc_final: 0.8888 (m) REVERT: D 975 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8929 (t0) REVERT: D 1037 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.6947 (p0) REVERT: D 1068 LEU cc_start: 0.8915 (tp) cc_final: 0.8503 (tt) REVERT: D 1162 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8173 (mttm) REVERT: D 1393 VAL cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (p) outliers start: 322 outliers final: 106 residues processed: 615 average time/residue: 0.2997 time to fit residues: 276.3275 Evaluate side-chains 351 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 218 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 188 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 63 HIS Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 343 ILE Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 305 ASP Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 859 THR Chi-restraints excluded: chain D residue 863 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 916 VAL Chi-restraints excluded: chain D residue 927 VAL Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 998 LYS Chi-restraints excluded: chain D residue 1037 ASN Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1057 VAL Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1071 ILE Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1162 LYS Chi-restraints excluded: chain D residue 1181 THR Chi-restraints excluded: chain D residue 1187 SER Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1240 ILE Chi-restraints excluded: chain D residue 1245 VAL Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1279 ASP Chi-restraints excluded: chain D residue 1364 LEU Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1385 VAL Chi-restraints excluded: chain D residue 1393 VAL Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 101 optimal weight: 0.0670 chunk 80 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 0.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 269 GLN B 273 ASN B 299 HIS C1360 ASN D 152 HIS D 167 ASN D 177 ASN D 309 GLN D 862 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16873 Z= 0.194 Angle : 0.680 9.607 22877 Z= 0.350 Chirality : 0.045 0.196 2548 Planarity : 0.005 0.069 2871 Dihedral : 11.506 75.185 2426 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 10.25 % Allowed : 20.61 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 1984 helix: -0.58 (0.17), residues: 778 sheet: -1.99 (0.31), residues: 231 loop : -3.30 (0.17), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 384 HIS 0.005 0.001 HIS D 126 PHE 0.030 0.002 PHE D 307 TYR 0.021 0.001 TYR A 319 ARG 0.005 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 228 time to evaluate : 2.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7053 (p0) cc_final: 0.6660 (t0) REVERT: A 256 ARG cc_start: 0.5316 (mtt180) cc_final: 0.3419 (mmm160) REVERT: A 357 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: A 398 LYS cc_start: 0.5591 (OUTLIER) cc_final: 0.5194 (tmtt) REVERT: A 408 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5701 (pp20) REVERT: A 446 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.5510 (p90) REVERT: A 486 ARG cc_start: 0.7036 (tpt90) cc_final: 0.5683 (mtp-110) REVERT: B 24 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7088 (tm-30) REVERT: B 33 CYS cc_start: 0.7601 (t) cc_final: 0.7118 (m) REVERT: B 83 MET cc_start: 0.7636 (tpp) cc_final: 0.7385 (ttm) REVERT: B 166 TYR cc_start: 0.8649 (m-80) cc_final: 0.8428 (m-10) REVERT: B 185 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8721 (mtmt) REVERT: B 313 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7629 (t70) REVERT: C 95 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: C 159 GLN cc_start: 0.6809 (OUTLIER) cc_final: 0.6274 (mp10) REVERT: C 223 MET cc_start: 0.7126 (tmm) cc_final: 0.6822 (tmm) REVERT: C 294 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7267 (tt0) REVERT: C 371 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6478 (tm-30) REVERT: C 1392 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7244 (mtpt) REVERT: C 1423 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7437 (ptt-90) REVERT: D 24 LYS cc_start: 0.8197 (pttp) cc_final: 0.7627 (mttt) REVERT: D 25 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7786 (tttt) REVERT: D 34 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.5389 (mmmt) REVERT: D 197 MET cc_start: 0.7737 (ppp) cc_final: 0.6869 (ppp) REVERT: D 228 ILE cc_start: 0.8805 (pt) cc_final: 0.8390 (mt) REVERT: D 237 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7626 (mtmm) REVERT: D 296 CYS cc_start: 0.7639 (t) cc_final: 0.7040 (m) REVERT: D 307 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7641 (m-10) REVERT: D 860 ASP cc_start: 0.7911 (t0) cc_final: 0.7475 (t0) REVERT: D 863 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8230 (pt) REVERT: D 994 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7400 (mt) REVERT: D 1037 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.6982 (p0) REVERT: D 1223 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8326 (mt) outliers start: 189 outliers final: 104 residues processed: 385 average time/residue: 0.2672 time to fit residues: 160.7112 Evaluate side-chains 310 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 187 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 398 LYS Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 59 MET Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 46 PHE Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 863 ILE Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 923 GLU Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 958 PHE Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 998 LYS Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1037 ASN Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1221 ASN Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1279 ASP Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 161 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 HIS B 291 GLN C 270 ASN D 144 ASN D 177 ASN D 273 HIS D 298 GLN D 862 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16873 Z= 0.180 Angle : 0.638 8.713 22877 Z= 0.325 Chirality : 0.044 0.209 2548 Planarity : 0.004 0.064 2871 Dihedral : 9.868 67.626 2334 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 8.73 % Allowed : 22.29 % Favored : 68.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 1984 helix: 0.17 (0.18), residues: 773 sheet: -1.73 (0.32), residues: 234 loop : -3.06 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 149 HIS 0.004 0.001 HIS D 126 PHE 0.023 0.001 PHE D 307 TYR 0.016 0.001 TYR A 236 ARG 0.017 0.000 ARG D 941 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 203 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7124 (p0) cc_final: 0.6664 (t0) REVERT: A 88 LYS cc_start: 0.5959 (mtpt) cc_final: 0.5750 (mmmt) REVERT: A 256 ARG cc_start: 0.5199 (mtt180) cc_final: 0.3321 (mmm160) REVERT: A 357 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: A 359 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 408 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5454 (pp20) REVERT: A 486 ARG cc_start: 0.7086 (tpt90) cc_final: 0.5666 (mtp-110) REVERT: B 24 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7044 (tm-30) REVERT: B 80 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7961 (t80) REVERT: B 83 MET cc_start: 0.7718 (tpp) cc_final: 0.7411 (ttm) REVERT: B 185 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8679 (mtmt) REVERT: B 313 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7677 (t70) REVERT: C 145 LYS cc_start: 0.7948 (mmtm) cc_final: 0.7635 (tppt) REVERT: C 159 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6195 (mp10) REVERT: C 281 SER cc_start: 0.8938 (OUTLIER) cc_final: 0.8726 (t) REVERT: C 294 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7379 (tt0) REVERT: C 1392 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7260 (mtpt) REVERT: C 1418 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8564 (t0) REVERT: C 1423 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7406 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8172 (OUTLIER) cc_final: 0.7883 (p90) REVERT: D 24 LYS cc_start: 0.8210 (pttp) cc_final: 0.7615 (mttt) REVERT: D 25 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7903 (tttt) REVERT: D 34 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.5409 (mmmt) REVERT: D 197 MET cc_start: 0.7930 (ppp) cc_final: 0.7074 (ppp) REVERT: D 237 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7684 (mmpt) REVERT: D 307 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7511 (m-10) REVERT: D 994 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7325 (mt) REVERT: D 1037 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6963 (p0) REVERT: D 1068 LEU cc_start: 0.8621 (tp) cc_final: 0.8244 (tt) REVERT: D 1096 MET cc_start: 0.8322 (mmm) cc_final: 0.8104 (mtt) REVERT: D 1223 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8347 (mt) outliers start: 161 outliers final: 102 residues processed: 338 average time/residue: 0.2526 time to fit residues: 133.5933 Evaluate side-chains 299 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 178 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 840 VAL Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 923 GLU Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1037 ASN Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1181 THR Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1221 ASN Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1279 ASP Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1364 LEU Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 178 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 181 optimal weight: 3.9990 chunk 192 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 172 optimal weight: 0.0980 chunk 51 optimal weight: 0.9990 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 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN A 460 HIS B 293 GLN D 862 ASN D 975 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16873 Z= 0.159 Angle : 0.599 9.023 22877 Z= 0.303 Chirality : 0.043 0.218 2548 Planarity : 0.004 0.058 2871 Dihedral : 9.051 58.176 2314 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 8.30 % Allowed : 22.89 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.19), residues: 1984 helix: 0.68 (0.19), residues: 772 sheet: -1.56 (0.32), residues: 237 loop : -2.86 (0.18), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 264 HIS 0.003 0.001 HIS D 126 PHE 0.021 0.001 PHE D 46 TYR 0.019 0.001 TYR A 402 ARG 0.004 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 197 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.5991 (mtpt) cc_final: 0.5761 (mmmt) REVERT: A 256 ARG cc_start: 0.4975 (mtt180) cc_final: 0.3209 (mmm160) REVERT: A 262 MET cc_start: 0.6582 (tpt) cc_final: 0.6350 (tpt) REVERT: A 324 VAL cc_start: 0.6843 (OUTLIER) cc_final: 0.6539 (m) REVERT: A 349 TRP cc_start: 0.8312 (t-100) cc_final: 0.8056 (t-100) REVERT: A 357 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8193 (tm-30) REVERT: A 359 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8218 (tt) REVERT: A 408 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5592 (pp20) REVERT: A 446 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.5624 (p90) REVERT: A 486 ARG cc_start: 0.7116 (tpt90) cc_final: 0.5648 (mtp-110) REVERT: B 24 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7080 (tm-30) REVERT: B 80 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7943 (t80) REVERT: B 83 MET cc_start: 0.7637 (tpp) cc_final: 0.7429 (ttm) REVERT: B 185 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8740 (mtmt) REVERT: B 313 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7722 (t70) REVERT: C 145 LYS cc_start: 0.7911 (mmtm) cc_final: 0.7633 (tppt) REVERT: C 281 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8671 (t) REVERT: C 294 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: C 1380 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.7071 (mtp) REVERT: C 1392 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7166 (mtmt) REVERT: C 1418 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8635 (t0) REVERT: C 1423 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7454 (ptt-90) REVERT: D 24 LYS cc_start: 0.8204 (pttp) cc_final: 0.7579 (mttt) REVERT: D 25 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7973 (tttt) REVERT: D 34 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.5337 (mmmt) REVERT: D 197 MET cc_start: 0.8010 (ppp) cc_final: 0.7179 (ppp) REVERT: D 237 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7887 (mmtt) REVERT: D 307 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: D 889 MET cc_start: 0.8146 (mmm) cc_final: 0.7924 (mtp) REVERT: D 994 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7189 (mt) REVERT: D 1037 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.7045 (p0) REVERT: D 1066 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8488 (pt) REVERT: D 1221 ASN cc_start: 0.8217 (m-40) cc_final: 0.7979 (m110) REVERT: D 1223 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8298 (mt) REVERT: D 1233 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.6508 (ttm170) outliers start: 153 outliers final: 98 residues processed: 322 average time/residue: 0.2540 time to fit residues: 127.7069 Evaluate side-chains 294 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 175 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 481 LYS Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1380 MET Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 834 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 975 ASN Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 998 LYS Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1037 ASN Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 160 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 164 optimal weight: 0.0970 chunk 132 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 HIS C 85 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16873 Z= 0.160 Angle : 0.597 13.471 22877 Z= 0.299 Chirality : 0.043 0.252 2548 Planarity : 0.004 0.054 2871 Dihedral : 8.705 58.933 2299 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 8.79 % Allowed : 22.99 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1984 helix: 0.89 (0.19), residues: 775 sheet: -1.44 (0.32), residues: 238 loop : -2.71 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 264 HIS 0.006 0.001 HIS A 460 PHE 0.017 0.001 PHE D 46 TYR 0.013 0.001 TYR C 178 ARG 0.003 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 186 time to evaluate : 2.126 Fit side-chains revert: symmetry clash REVERT: A 88 LYS cc_start: 0.6010 (mtpt) cc_final: 0.5790 (mmmt) REVERT: A 256 ARG cc_start: 0.4914 (mtt180) cc_final: 0.3170 (mmm160) REVERT: A 262 MET cc_start: 0.6595 (tpt) cc_final: 0.6361 (tpt) REVERT: A 324 VAL cc_start: 0.6711 (OUTLIER) cc_final: 0.6504 (m) REVERT: A 349 TRP cc_start: 0.8261 (t-100) cc_final: 0.8060 (t-100) REVERT: A 357 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8178 (tm-30) REVERT: A 359 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8151 (tt) REVERT: A 408 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5605 (pp20) REVERT: A 446 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.5546 (p90) REVERT: A 486 ARG cc_start: 0.7134 (tpt90) cc_final: 0.5645 (mtp-110) REVERT: B 24 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7084 (tm-30) REVERT: B 80 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7941 (t80) REVERT: B 83 MET cc_start: 0.7659 (tpp) cc_final: 0.7446 (ttm) REVERT: B 166 TYR cc_start: 0.8534 (m-80) cc_final: 0.8002 (m-80) REVERT: B 185 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8717 (mtmt) REVERT: B 313 HIS cc_start: 0.8025 (OUTLIER) cc_final: 0.7720 (t70) REVERT: C 145 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7635 (tppt) REVERT: C 281 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8654 (t) REVERT: C 294 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: C 371 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: C 1380 MET cc_start: 0.7513 (mtp) cc_final: 0.7188 (mtp) REVERT: C 1392 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7137 (mtmt) REVERT: C 1418 ASP cc_start: 0.8865 (OUTLIER) cc_final: 0.8599 (t0) REVERT: C 1423 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7411 (ptt-90) REVERT: C 1427 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7872 (p90) REVERT: D 24 LYS cc_start: 0.8267 (pttp) cc_final: 0.7638 (mttt) REVERT: D 25 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (tttt) REVERT: D 34 LYS cc_start: 0.6971 (OUTLIER) cc_final: 0.5253 (mmmt) REVERT: D 197 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7293 (ppp) REVERT: D 237 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7870 (mmtt) REVERT: D 307 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7346 (m-10) REVERT: D 832 ILE cc_start: 0.9116 (pp) cc_final: 0.8886 (pt) REVERT: D 889 MET cc_start: 0.8213 (mmm) cc_final: 0.7962 (mtp) REVERT: D 994 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7262 (tt) REVERT: D 1037 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.7086 (p0) REVERT: D 1066 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8503 (pt) REVERT: D 1223 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8262 (mt) REVERT: D 1233 ARG cc_start: 0.7823 (tpp-160) cc_final: 0.6556 (ttm170) REVERT: D 1282 ARG cc_start: 0.7712 (ptp-170) cc_final: 0.7410 (mtt180) REVERT: D 1283 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6867 (tt) REVERT: D 1293 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7033 (mp10) outliers start: 162 outliers final: 106 residues processed: 319 average time/residue: 0.2550 time to fit residues: 127.9755 Evaluate side-chains 304 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 172 time to evaluate : 1.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 278 HIS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain C residue 1427 HIS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1037 ASN Chi-restraints excluded: chain D residue 1066 LEU Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1181 THR Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1223 ILE Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1242 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1283 LEU Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1298 ILE Chi-restraints excluded: chain D residue 1311 HIS Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1388 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 0.4980 chunk 173 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 0.0670 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 GLN B 273 ASN C 85 GLN D 43 GLN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16873 Z= 0.173 Angle : 0.599 12.091 22877 Z= 0.299 Chirality : 0.043 0.197 2548 Planarity : 0.004 0.065 2871 Dihedral : 8.410 59.816 2287 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 8.35 % Allowed : 23.97 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 1984 helix: 1.12 (0.19), residues: 770 sheet: -1.30 (0.32), residues: 240 loop : -2.63 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 264 HIS 0.003 0.001 HIS C1372 PHE 0.019 0.001 PHE D1210 TYR 0.021 0.001 TYR A 418 ARG 0.005 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 185 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7301 (p0) cc_final: 0.6607 (t0) REVERT: A 230 LYS cc_start: 0.7786 (tptm) cc_final: 0.7168 (mtmt) REVERT: A 256 ARG cc_start: 0.4913 (mtt180) cc_final: 0.3173 (mmm160) REVERT: A 262 MET cc_start: 0.6612 (tpt) cc_final: 0.6327 (tpt) REVERT: A 349 TRP cc_start: 0.8229 (t-100) cc_final: 0.8028 (t-100) REVERT: A 359 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8151 (tt) REVERT: A 408 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.5568 (pp20) REVERT: A 446 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.5487 (p90) REVERT: A 486 ARG cc_start: 0.7153 (tpt90) cc_final: 0.5772 (mtp-110) REVERT: B 24 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7078 (tm-30) REVERT: B 80 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7966 (t80) REVERT: B 83 MET cc_start: 0.7709 (tpp) cc_final: 0.7491 (ttm) REVERT: B 126 TYR cc_start: 0.8684 (t80) cc_final: 0.8340 (t80) REVERT: B 166 TYR cc_start: 0.8507 (m-80) cc_final: 0.8004 (m-80) REVERT: B 185 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8709 (mtmt) REVERT: C 145 LYS cc_start: 0.7962 (mmtm) cc_final: 0.7750 (tppt) REVERT: C 159 GLN cc_start: 0.6806 (OUTLIER) cc_final: 0.6431 (mm-40) REVERT: C 281 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8687 (t) REVERT: C 294 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: C 371 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6640 (mm-30) REVERT: C 1392 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7159 (mtmt) REVERT: C 1418 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8617 (t0) REVERT: D 24 LYS cc_start: 0.8266 (pttp) cc_final: 0.7692 (mttt) REVERT: D 25 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8062 (tttt) REVERT: D 34 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.5360 (mmmt) REVERT: D 197 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7531 (ppp) REVERT: D 994 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7297 (tt) REVERT: D 1061 MET cc_start: 0.7711 (tmm) cc_final: 0.7254 (tpp) REVERT: D 1218 THR cc_start: 0.9408 (p) cc_final: 0.9098 (t) REVERT: D 1233 ARG cc_start: 0.7914 (tpp-160) cc_final: 0.6579 (ttm170) REVERT: D 1282 ARG cc_start: 0.7742 (ptp-170) cc_final: 0.7418 (mtt180) REVERT: D 1293 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7023 (mp10) REVERT: D 1348 THR cc_start: 0.8608 (OUTLIER) cc_final: 0.8204 (t) outliers start: 154 outliers final: 106 residues processed: 313 average time/residue: 0.2538 time to fit residues: 125.2315 Evaluate side-chains 292 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 169 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 383 ASN Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1181 THR Chi-restraints excluded: chain D residue 1192 ASP Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1348 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 185 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 5.9990 chunk 140 optimal weight: 0.0870 chunk 108 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 191 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN C 274 ASN ** D 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 862 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16873 Z= 0.179 Angle : 0.623 13.360 22877 Z= 0.305 Chirality : 0.043 0.191 2548 Planarity : 0.004 0.055 2871 Dihedral : 7.956 57.362 2273 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 8.13 % Allowed : 24.57 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.19), residues: 1984 helix: 1.29 (0.19), residues: 770 sheet: -1.23 (0.33), residues: 240 loop : -2.59 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 264 HIS 0.003 0.001 HIS B 221 PHE 0.030 0.001 PHE D 46 TYR 0.014 0.001 TYR A 418 ARG 0.002 0.000 ARG A 485 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 186 time to evaluate : 1.824 Fit side-chains revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7393 (p0) cc_final: 0.6645 (t0) REVERT: A 88 LYS cc_start: 0.6199 (mtpt) cc_final: 0.5930 (mmpt) REVERT: A 256 ARG cc_start: 0.4872 (mtt180) cc_final: 0.3073 (mmm160) REVERT: A 262 MET cc_start: 0.6587 (tpt) cc_final: 0.6301 (tpt) REVERT: A 357 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: A 359 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 408 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5674 (pp20) REVERT: A 446 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.5571 (p90) REVERT: A 486 ARG cc_start: 0.7134 (tpt90) cc_final: 0.5731 (mtp-110) REVERT: B 24 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 80 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7846 (t80) REVERT: B 83 MET cc_start: 0.7700 (tpp) cc_final: 0.7487 (ttm) REVERT: B 126 TYR cc_start: 0.8762 (t80) cc_final: 0.8311 (t80) REVERT: B 166 TYR cc_start: 0.8489 (m-80) cc_final: 0.8026 (m-10) REVERT: B 185 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8714 (mtmt) REVERT: B 313 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7715 (t70) REVERT: C 145 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7767 (tppt) REVERT: C 274 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8032 (t0) REVERT: C 281 SER cc_start: 0.8855 (OUTLIER) cc_final: 0.8583 (t) REVERT: C 286 MET cc_start: 0.8762 (mmt) cc_final: 0.8230 (mmp) REVERT: C 342 TYR cc_start: 0.4278 (m-80) cc_final: 0.3997 (m-80) REVERT: C 371 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6564 (mm-30) REVERT: C 1387 SER cc_start: 0.8921 (t) cc_final: 0.8576 (p) REVERT: C 1392 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7162 (mtmt) REVERT: C 1418 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8514 (t0) REVERT: D 24 LYS cc_start: 0.8267 (pttp) cc_final: 0.7718 (mttt) REVERT: D 25 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8066 (tttt) REVERT: D 34 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.5152 (mtpp) REVERT: D 197 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7607 (ppp) REVERT: D 994 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7326 (tt) REVERT: D 1061 MET cc_start: 0.7656 (tmm) cc_final: 0.7214 (tpp) REVERT: D 1073 MET cc_start: 0.8701 (tpp) cc_final: 0.8230 (tpt) REVERT: D 1218 THR cc_start: 0.9414 (p) cc_final: 0.9098 (t) REVERT: D 1233 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.6590 (ttm170) REVERT: D 1282 ARG cc_start: 0.7742 (ptp-170) cc_final: 0.7479 (mtt180) REVERT: D 1293 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: D 1348 THR cc_start: 0.8640 (OUTLIER) cc_final: 0.8249 (t) outliers start: 150 outliers final: 105 residues processed: 304 average time/residue: 0.2462 time to fit residues: 118.3624 Evaluate side-chains 301 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 177 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1181 THR Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1279 ASP Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1348 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 118 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 121 optimal weight: 0.0570 chunk 130 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 174 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 862 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16873 Z= 0.161 Angle : 0.610 11.765 22877 Z= 0.300 Chirality : 0.043 0.176 2548 Planarity : 0.004 0.054 2871 Dihedral : 7.769 57.149 2269 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 7.70 % Allowed : 25.54 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.19), residues: 1984 helix: 1.36 (0.19), residues: 770 sheet: -1.17 (0.33), residues: 234 loop : -2.55 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 349 HIS 0.002 0.001 HIS C1372 PHE 0.024 0.001 PHE C 275 TYR 0.016 0.001 TYR A 402 ARG 0.002 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 183 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7423 (p0) cc_final: 0.6644 (t0) REVERT: A 88 LYS cc_start: 0.6180 (mtpt) cc_final: 0.5924 (mmpt) REVERT: A 256 ARG cc_start: 0.4856 (mtt180) cc_final: 0.3065 (mmm160) REVERT: A 262 MET cc_start: 0.6534 (tpt) cc_final: 0.6265 (tpt) REVERT: A 357 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: A 359 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8196 (tt) REVERT: A 408 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5652 (pp20) REVERT: A 446 TYR cc_start: 0.7495 (OUTLIER) cc_final: 0.5763 (p90) REVERT: A 486 ARG cc_start: 0.7140 (tpt90) cc_final: 0.5746 (mtp-110) REVERT: B 24 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7068 (tm-30) REVERT: B 80 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7857 (t80) REVERT: B 126 TYR cc_start: 0.8709 (t80) cc_final: 0.8331 (t80) REVERT: B 166 TYR cc_start: 0.8482 (m-80) cc_final: 0.8031 (m-10) REVERT: B 185 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8654 (mtpt) REVERT: B 313 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7708 (t70) REVERT: C 159 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6483 (mm-40) REVERT: C 274 ASN cc_start: 0.8675 (p0) cc_final: 0.8127 (t0) REVERT: C 281 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8621 (t) REVERT: C 286 MET cc_start: 0.8778 (mmt) cc_final: 0.8572 (mmp) REVERT: C 294 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: C 371 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6630 (mm-30) REVERT: C 1387 SER cc_start: 0.8916 (t) cc_final: 0.8588 (p) REVERT: C 1392 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7192 (mtmt) REVERT: C 1418 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8539 (t0) REVERT: D 24 LYS cc_start: 0.8260 (pttp) cc_final: 0.7727 (mttt) REVERT: D 25 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8081 (tttt) REVERT: D 34 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.4983 (mtpt) REVERT: D 197 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7592 (ppp) REVERT: D 994 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7271 (tt) REVERT: D 1061 MET cc_start: 0.7621 (tmm) cc_final: 0.7151 (tpp) REVERT: D 1073 MET cc_start: 0.8702 (tpp) cc_final: 0.8156 (tpt) REVERT: D 1218 THR cc_start: 0.9421 (p) cc_final: 0.9111 (t) REVERT: D 1233 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.6489 (ttm170) REVERT: D 1282 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.7435 (mtt180) REVERT: D 1293 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7024 (mp10) REVERT: D 1348 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8241 (t) outliers start: 142 outliers final: 105 residues processed: 298 average time/residue: 0.2770 time to fit residues: 131.0883 Evaluate side-chains 300 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 176 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 29 TRP Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 158 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 273 HIS Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 831 ASP Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1007 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1037 ASN Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1348 THR Chi-restraints excluded: chain D residue 1370 LEU Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 183 optimal weight: 3.9990 chunk 167 optimal weight: 0.0040 chunk 178 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN C 270 ASN D1310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16873 Z= 0.176 Angle : 0.611 10.200 22877 Z= 0.302 Chirality : 0.043 0.168 2548 Planarity : 0.004 0.055 2871 Dihedral : 7.660 56.795 2267 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 7.21 % Allowed : 25.81 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1984 helix: 1.41 (0.19), residues: 772 sheet: -1.31 (0.33), residues: 226 loop : -2.46 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 349 HIS 0.003 0.001 HIS D 823 PHE 0.037 0.001 PHE D 46 TYR 0.021 0.001 TYR C 227 ARG 0.002 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 187 time to evaluate : 1.928 Fit side-chains revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7461 (p0) cc_final: 0.6630 (t0) REVERT: A 88 LYS cc_start: 0.6143 (mtpt) cc_final: 0.5856 (mmpt) REVERT: A 230 LYS cc_start: 0.7777 (tptp) cc_final: 0.7264 (ptpt) REVERT: A 256 ARG cc_start: 0.4867 (mtt180) cc_final: 0.3076 (mmm160) REVERT: A 262 MET cc_start: 0.6514 (tpt) cc_final: 0.6245 (tpt) REVERT: A 357 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8104 (tm-30) REVERT: A 359 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 408 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5656 (pp20) REVERT: A 446 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.5828 (p90) REVERT: A 486 ARG cc_start: 0.7109 (tpt90) cc_final: 0.5701 (mtp-110) REVERT: B 24 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7083 (tm-30) REVERT: B 80 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7974 (t80) REVERT: B 126 TYR cc_start: 0.8713 (t80) cc_final: 0.8323 (t80) REVERT: B 166 TYR cc_start: 0.8474 (m-80) cc_final: 0.8005 (m-10) REVERT: B 185 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8655 (mtpt) REVERT: B 313 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7795 (t70) REVERT: C 159 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6520 (mm-40) REVERT: C 218 LYS cc_start: 0.8224 (tppt) cc_final: 0.7967 (tppt) REVERT: C 227 TYR cc_start: 0.6304 (p90) cc_final: 0.6062 (p90) REVERT: C 274 ASN cc_start: 0.8747 (p0) cc_final: 0.8372 (t0) REVERT: C 281 SER cc_start: 0.8891 (OUTLIER) cc_final: 0.8620 (t) REVERT: C 294 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: C 371 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6676 (mm-30) REVERT: C 1387 SER cc_start: 0.8891 (t) cc_final: 0.8584 (p) REVERT: C 1392 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7241 (mtmt) REVERT: C 1418 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8521 (t0) REVERT: C 1423 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7407 (ptt-90) REVERT: D 24 LYS cc_start: 0.8252 (pttp) cc_final: 0.7675 (mttt) REVERT: D 25 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8059 (tttt) REVERT: D 34 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.5035 (mtpt) REVERT: D 197 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7585 (ppp) REVERT: D 994 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7304 (tt) REVERT: D 1061 MET cc_start: 0.7644 (tmm) cc_final: 0.7139 (tpp) REVERT: D 1073 MET cc_start: 0.8617 (tpp) cc_final: 0.8027 (tpt) REVERT: D 1218 THR cc_start: 0.9416 (p) cc_final: 0.9108 (t) REVERT: D 1229 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8439 (tm) REVERT: D 1233 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.6536 (ttm170) REVERT: D 1282 ARG cc_start: 0.7743 (ptp-170) cc_final: 0.7466 (mtt180) REVERT: D 1293 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7036 (mp10) REVERT: D 1348 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8265 (t) outliers start: 133 outliers final: 93 residues processed: 297 average time/residue: 0.2580 time to fit residues: 120.2357 Evaluate side-chains 296 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 182 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 78 CYS Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 14 ASP Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 371 GLU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1354 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain C residue 1423 ARG Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 831 ASP Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 951 SER Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1026 VAL Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1215 LEU Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1279 ASP Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1348 THR Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 115 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 198 optimal weight: 0.0670 chunk 182 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 0.0070 chunk 96 optimal weight: 5.9990 chunk 125 optimal weight: 0.0570 chunk 168 optimal weight: 0.6980 overall best weight: 0.3254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 16873 Z= 0.148 Angle : 0.622 13.791 22877 Z= 0.302 Chirality : 0.043 0.169 2548 Planarity : 0.004 0.053 2871 Dihedral : 7.352 56.848 2260 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 6.07 % Allowed : 27.33 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1984 helix: 1.53 (0.19), residues: 767 sheet: -1.19 (0.33), residues: 226 loop : -2.34 (0.20), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP A 349 HIS 0.003 0.000 HIS C 226 PHE 0.036 0.001 PHE D 46 TYR 0.033 0.001 TYR C 227 ARG 0.002 0.000 ARG A 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3968 Ramachandran restraints generated. 1984 Oldfield, 0 Emsley, 1984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 191 time to evaluate : 2.046 Fit side-chains revert: symmetry clash REVERT: A 52 ASN cc_start: 0.7449 (p0) cc_final: 0.6616 (t0) REVERT: A 88 LYS cc_start: 0.6067 (mtpt) cc_final: 0.5823 (mmpt) REVERT: A 230 LYS cc_start: 0.7776 (tptp) cc_final: 0.7255 (ptpt) REVERT: A 256 ARG cc_start: 0.4791 (mtt180) cc_final: 0.3004 (mmm160) REVERT: A 262 MET cc_start: 0.6343 (tpt) cc_final: 0.6131 (tpt) REVERT: A 347 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6809 (t0) REVERT: A 357 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: A 359 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7978 (tt) REVERT: A 408 GLU cc_start: 0.6657 (OUTLIER) cc_final: 0.5627 (pp20) REVERT: A 446 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.5734 (p90) REVERT: A 486 ARG cc_start: 0.7105 (tpt90) cc_final: 0.5674 (mtp-110) REVERT: B 24 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7062 (tm-30) REVERT: B 80 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7898 (t80) REVERT: B 126 TYR cc_start: 0.8649 (t80) cc_final: 0.8340 (t80) REVERT: B 166 TYR cc_start: 0.8446 (m-80) cc_final: 0.7991 (m-10) REVERT: B 185 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8717 (mtmt) REVERT: C 122 THR cc_start: 0.5765 (OUTLIER) cc_final: 0.5446 (p) REVERT: C 159 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6573 (mm-40) REVERT: C 218 LYS cc_start: 0.8189 (tppt) cc_final: 0.7883 (tppt) REVERT: C 274 ASN cc_start: 0.8649 (p0) cc_final: 0.8387 (t0) REVERT: C 281 SER cc_start: 0.8884 (OUTLIER) cc_final: 0.8644 (t) REVERT: C 294 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: C 1387 SER cc_start: 0.8839 (t) cc_final: 0.8537 (p) REVERT: C 1392 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7204 (mtmt) REVERT: C 1418 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8493 (t0) REVERT: D 24 LYS cc_start: 0.8229 (pttp) cc_final: 0.7663 (mttt) REVERT: D 25 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8020 (tttt) REVERT: D 34 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.5034 (mtpp) REVERT: D 197 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7622 (ppp) REVERT: D 994 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7224 (tt) REVERT: D 1061 MET cc_start: 0.7649 (tmm) cc_final: 0.7137 (tpp) REVERT: D 1218 THR cc_start: 0.9418 (p) cc_final: 0.9104 (t) REVERT: D 1229 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8467 (tm) REVERT: D 1233 ARG cc_start: 0.7805 (tpp-160) cc_final: 0.6483 (ttm170) REVERT: D 1261 LEU cc_start: 0.8461 (mm) cc_final: 0.7776 (tp) REVERT: D 1282 ARG cc_start: 0.7762 (ptp-170) cc_final: 0.7499 (mtt180) REVERT: D 1293 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7088 (mp10) outliers start: 112 outliers final: 79 residues processed: 276 average time/residue: 0.2532 time to fit residues: 109.6628 Evaluate side-chains 279 residues out of total 1844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 181 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 215 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 408 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 446 TYR Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain B residue 67 HIS Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 56 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 159 GLN Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 328 TYR Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 387 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 1375 VAL Chi-restraints excluded: chain C residue 1392 LYS Chi-restraints excluded: chain C residue 1418 ASP Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 25 LYS Chi-restraints excluded: chain D residue 27 ASN Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 258 TYR Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 307 PHE Chi-restraints excluded: chain D residue 831 ASP Chi-restraints excluded: chain D residue 835 THR Chi-restraints excluded: chain D residue 867 LEU Chi-restraints excluded: chain D residue 869 ILE Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 935 ILE Chi-restraints excluded: chain D residue 948 ASN Chi-restraints excluded: chain D residue 988 ASN Chi-restraints excluded: chain D residue 994 LEU Chi-restraints excluded: chain D residue 1025 ASN Chi-restraints excluded: chain D residue 1039 THR Chi-restraints excluded: chain D residue 1041 THR Chi-restraints excluded: chain D residue 1082 THR Chi-restraints excluded: chain D residue 1102 VAL Chi-restraints excluded: chain D residue 1119 THR Chi-restraints excluded: chain D residue 1145 ILE Chi-restraints excluded: chain D residue 1193 ASP Chi-restraints excluded: chain D residue 1229 LEU Chi-restraints excluded: chain D residue 1249 ASP Chi-restraints excluded: chain D residue 1256 ILE Chi-restraints excluded: chain D residue 1293 GLN Chi-restraints excluded: chain D residue 1330 THR Chi-restraints excluded: chain D residue 1377 HIS Chi-restraints excluded: chain D residue 1397 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 48 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 162 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 138 optimal weight: 0.4980 chunk 9 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 228 ASN C 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107892 restraints weight = 33782.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109608 restraints weight = 23749.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110310 restraints weight = 17352.944| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16873 Z= 0.158 Angle : 0.622 13.118 22877 Z= 0.303 Chirality : 0.043 0.174 2548 Planarity : 0.004 0.054 2871 Dihedral : 6.966 55.714 2252 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 5.53 % Allowed : 27.82 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1984 helix: 1.62 (0.19), residues: 763 sheet: -1.17 (0.33), residues: 226 loop : -2.30 (0.20), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 349 HIS 0.003 0.000 HIS C 226 PHE 0.035 0.001 PHE D 46 TYR 0.023 0.001 TYR C 227 ARG 0.002 0.000 ARG A 261 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.45 seconds wall clock time: 67 minutes 19.18 seconds (4039.18 seconds total)