Starting phenix.real_space_refine on Fri Jun 13 07:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiq_9997/06_2025/6kiq_9997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiq_9997/06_2025/6kiq_9997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kiq_9997/06_2025/6kiq_9997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiq_9997/06_2025/6kiq_9997.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiq_9997/06_2025/6kiq_9997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiq_9997/06_2025/6kiq_9997.cif" } resolution = 3.62 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= 0.010 sd= 0.054 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 4827 2.51 5 N 1310 2.21 5 O 1458 1.98 5 H 7444 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15093 Number of models: 1 Model: "" Number of chains: 3 Chain: "a" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6375 Classifications: {'peptide': 412} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 392} Chain: "b" Number of atoms: 6584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6584 Classifications: {'peptide': 426} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain: "M" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2134 Classifications: {'peptide': 130} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Time building chain proxies: 8.40, per 1000 atoms: 0.56 Number of scatterers: 15093 At special positions: 0 Unit cell: (79.2, 106.92, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 1458 8.00 N 1310 7.00 C 4827 6.00 H 7444 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 54.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'a' and resid 1010 through 1029 removed outlier: 3.535A pdb=" N GLN a1015 " --> pdb=" O GLN a1011 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU a1022 " --> pdb=" O ASN a1018 " (cutoff:3.500A) Processing helix chain 'a' and resid 1046 through 1055 removed outlier: 3.800A pdb=" N VAL a1052 " --> pdb=" O VAL a1048 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR a1054 " --> pdb=" O ASP a1050 " (cutoff:3.500A) Processing helix chain 'a' and resid 1062 through 1064 No H-bonds generated for 'chain 'a' and resid 1062 through 1064' Processing helix chain 'a' and resid 1076 through 1082 removed outlier: 3.918A pdb=" N GLY a1080 " --> pdb=" O ASN a1076 " (cutoff:3.500A) Processing helix chain 'a' and resid 1082 through 1101 removed outlier: 4.515A pdb=" N GLU a1087 " --> pdb=" O THR a1083 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE a1088 " --> pdb=" O ILE a1084 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP a1090 " --> pdb=" O LYS a1086 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU a1091 " --> pdb=" O GLU a1087 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG a1095 " --> pdb=" O LEU a1091 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE a1096 " --> pdb=" O VAL a1092 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG a1097 " --> pdb=" O LEU a1093 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP a1101 " --> pdb=" O ARG a1097 " (cutoff:3.500A) Processing helix chain 'a' and resid 1121 through 1135 removed outlier: 3.727A pdb=" N GLU a1129 " --> pdb=" O SER a1125 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL a1133 " --> pdb=" O GLU a1129 " (cutoff:3.500A) Processing helix chain 'a' and resid 1156 through 1170 removed outlier: 3.561A pdb=" N THR a1165 " --> pdb=" O SER a1161 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N HIS a1166 " --> pdb=" O ILE a1162 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR a1167 " --> pdb=" O LEU a1163 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU a1170 " --> pdb=" O HIS a1166 " (cutoff:3.500A) Processing helix chain 'a' and resid 1179 through 1190 removed outlier: 3.994A pdb=" N ASP a1185 " --> pdb=" O GLU a1181 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE a1186 " --> pdb=" O ALA a1182 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS a1187 " --> pdb=" O ILE a1183 " (cutoff:3.500A) Processing helix chain 'a' and resid 1197 through 1217 removed outlier: 3.600A pdb=" N LEU a1201 " --> pdb=" O THR a1197 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG a1203 " --> pdb=" O THR a1199 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN a1207 " --> pdb=" O ARG a1203 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER a1210 " --> pdb=" O GLY a1206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE a1212 " --> pdb=" O ILE a1208 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR a1213 " --> pdb=" O VAL a1209 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA a1214 " --> pdb=" O SER a1210 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER a1215 " --> pdb=" O SER a1211 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU a1216 " --> pdb=" O ILE a1212 " (cutoff:3.500A) Processing helix chain 'a' and resid 1225 through 1233 removed outlier: 3.681A pdb=" N PHE a1229 " --> pdb=" O ASP a1225 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN a1230 " --> pdb=" O LEU a1226 " (cutoff:3.500A) Processing helix chain 'a' and resid 1261 through 1271 removed outlier: 3.655A pdb=" N ASN a1267 " --> pdb=" O ALA a1263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS a1269 " --> pdb=" O ILE a1265 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE a1270 " --> pdb=" O THR a1266 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU a1271 " --> pdb=" O ASN a1267 " (cutoff:3.500A) Processing helix chain 'a' and resid 1280 through 1284 removed outlier: 4.332A pdb=" N HIS a1283 " --> pdb=" O ASP a1280 " (cutoff:3.500A) Processing helix chain 'a' and resid 1298 through 1311 removed outlier: 3.711A pdb=" N VAL a1302 " --> pdb=" O VAL a1298 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA a1307 " --> pdb=" O ASN a1303 " (cutoff:3.500A) Processing helix chain 'a' and resid 1358 through 1376 removed outlier: 3.508A pdb=" N ARG a1364 " --> pdb=" O GLU a1360 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU a1365 " --> pdb=" O ALA a1361 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU a1371 " --> pdb=" O HIS a1367 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET a1372 " --> pdb=" O LYS a1368 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS a1375 " --> pdb=" O LEU a1371 " (cutoff:3.500A) Processing helix chain 'a' and resid 1379 through 1384 removed outlier: 3.554A pdb=" N GLY a1384 " --> pdb=" O HIS a1380 " (cutoff:3.500A) Processing helix chain 'a' and resid 1388 through 1404 removed outlier: 3.628A pdb=" N PHE a1392 " --> pdb=" O GLU a1388 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET a1399 " --> pdb=" O ALA a1395 " (cutoff:3.500A) Processing helix chain 'a' and resid 1404 through 1409 Processing helix chain 'b' and resid 10 through 27 removed outlier: 4.299A pdb=" N GLY b 17 " --> pdb=" O GLY b 13 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS b 19 " --> pdb=" O GLN b 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU b 22 " --> pdb=" O ALA b 18 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 47 removed outlier: 4.145A pdb=" N LEU b 44 " --> pdb=" O SER b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 52 Processing helix chain 'b' and resid 74 through 79 Processing helix chain 'b' and resid 88 through 90 No H-bonds generated for 'chain 'b' and resid 88 through 90' Processing helix chain 'b' and resid 103 through 107 Processing helix chain 'b' and resid 110 through 115 Processing helix chain 'b' and resid 115 through 127 removed outlier: 4.246A pdb=" N VAL b 121 " --> pdb=" O SER b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 148 removed outlier: 4.224A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY b 148 " --> pdb=" O GLY b 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 143 through 148' Processing helix chain 'b' and resid 148 through 161 removed outlier: 4.334A pdb=" N SER b 155 " --> pdb=" O THR b 151 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS b 156 " --> pdb=" O LEU b 152 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU b 159 " --> pdb=" O SER b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 195 removed outlier: 3.589A pdb=" N ASN b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER b 190 " --> pdb=" O ASN b 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS b 192 " --> pdb=" O THR b 188 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN b 193 " --> pdb=" O LEU b 189 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 215 removed outlier: 3.779A pdb=" N CYS b 213 " --> pdb=" O LEU b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 223 through 238 removed outlier: 3.520A pdb=" N LEU b 227 " --> pdb=" O THR b 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA b 233 " --> pdb=" O HIS b 229 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR b 234 " --> pdb=" O LEU b 230 " (cutoff:3.500A) Processing helix chain 'b' and resid 239 through 244 Processing helix chain 'b' and resid 251 through 258 removed outlier: 3.679A pdb=" N ALA b 256 " --> pdb=" O LEU b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 277 through 281 removed outlier: 3.636A pdb=" N GLN b 281 " --> pdb=" O ARG b 278 " (cutoff:3.500A) Processing helix chain 'b' and resid 288 through 296 Processing helix chain 'b' and resid 306 through 310 removed outlier: 3.545A pdb=" N HIS b 309 " --> pdb=" O ASP b 306 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 339 removed outlier: 3.596A pdb=" N VAL b 328 " --> pdb=" O SER b 324 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP b 329 " --> pdb=" O MET b 325 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU b 333 " --> pdb=" O ASP b 329 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN b 339 " --> pdb=" O VAL b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 340 through 343 removed outlier: 3.836A pdb=" N PHE b 343 " --> pdb=" O SER b 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 340 through 343' Processing helix chain 'b' and resid 381 through 383 No H-bonds generated for 'chain 'b' and resid 381 through 383' Processing helix chain 'b' and resid 384 through 400 removed outlier: 4.290A pdb=" N PHE b 388 " --> pdb=" O ILE b 384 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG b 390 " --> pdb=" O GLU b 386 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 410 Processing helix chain 'b' and resid 415 through 435 removed outlier: 3.662A pdb=" N VAL b 429 " --> pdb=" O MET b 425 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) Processing helix chain 'M' and resid 3103 through 3114 removed outlier: 3.589A pdb=" N GLN M3109 " --> pdb=" O ILE M3105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG M3110 " --> pdb=" O LEU M3106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS M3113 " --> pdb=" O GLN M3109 " (cutoff:3.500A) Processing helix chain 'M' and resid 3116 through 3126 removed outlier: 3.697A pdb=" N LEU M3120 " --> pdb=" O LYS M3116 " (cutoff:3.500A) Processing helix chain 'M' and resid 3130 through 3145 removed outlier: 3.813A pdb=" N VAL M3136 " --> pdb=" O GLY M3132 " (cutoff:3.500A) Processing helix chain 'M' and resid 3150 through 3159 Processing helix chain 'M' and resid 3161 through 3170 removed outlier: 4.393A pdb=" N HIS M3165 " --> pdb=" O ASP M3161 " (cutoff:3.500A) Processing helix chain 'M' and resid 3179 through 3189 Processing helix chain 'M' and resid 3195 through 3203 removed outlier: 3.515A pdb=" N ILE M3199 " --> pdb=" O THR M3195 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER M3203 " --> pdb=" O ILE M3199 " (cutoff:3.500A) Processing helix chain 'M' and resid 3205 through 3219 Processing sheet with id=AA1, first strand: chain 'a' and resid 1066 through 1068 removed outlier: 5.653A pdb=" N PHE a1041 " --> pdb=" O ILE a1067 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER a1006 " --> pdb=" O VAL a1040 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL a1042 " --> pdb=" O SER a1006 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N HIS a1008 " --> pdb=" O VAL a1042 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 1242 through 1243 removed outlier: 5.795A pdb=" N ASN a1354 " --> pdb=" O MET a1287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 1328 through 1330 removed outlier: 3.893A pdb=" N LEU a1292 " --> pdb=" O CYS a1350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 92 through 94 removed outlier: 6.436A pdb=" N LEU b 67 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL b 68 " --> pdb=" O HIS b 6 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN b 8 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU b 3 " --> pdb=" O GLN b 133 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE b 135 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL b 5 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU b 137 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE b 7 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS b 139 " --> pdb=" O ILE b 7 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA b 9 " --> pdb=" O HIS b 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE b 165 " --> pdb=" O GLN b 133 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N MET b 166 " --> pdb=" O GLU b 200 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR b 202 " --> pdb=" O MET b 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR b 168 " --> pdb=" O TYR b 202 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR b 201 " --> pdb=" O PHE b 268 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR b 376 " --> pdb=" O VAL b 318 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA b 354 " --> pdb=" O PHE b 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 55 through 56 285 hydrogen bonds defined for protein. 813 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: 5.99 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 7420 1.13 - 1.31: 1858 1.31 - 1.49: 3744 1.49 - 1.67: 2159 1.67 - 1.84: 84 Bond restraints: 15265 Sorted by residual: bond pdb=" CA PRO b 63 " pdb=" C PRO b 63 " ideal model delta sigma weight residual 1.521 1.375 0.146 1.21e-02 6.83e+03 1.46e+02 bond pdb=" CA TYR a1024 " pdb=" C TYR a1024 " ideal model delta sigma weight residual 1.523 1.364 0.159 1.34e-02 5.57e+03 1.41e+02 bond pdb=" C MET b 269 " pdb=" N PRO b 270 " ideal model delta sigma weight residual 1.331 1.179 0.152 1.31e-02 5.83e+03 1.34e+02 bond pdb=" CA CYS a1350 " pdb=" C CYS a1350 " ideal model delta sigma weight residual 1.526 1.390 0.135 1.22e-02 6.72e+03 1.23e+02 bond pdb=" CA VAL b 288 " pdb=" C VAL b 288 " ideal model delta sigma weight residual 1.524 1.409 0.115 1.05e-02 9.07e+03 1.21e+02 ... (remaining 15260 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 22696 4.17 - 8.34: 4270 8.34 - 12.51: 485 12.51 - 16.68: 52 16.68 - 20.85: 7 Bond angle restraints: 27510 Sorted by residual: angle pdb=" N THR a1231 " pdb=" CA THR a1231 " pdb=" C THR a1231 " ideal model delta sigma weight residual 111.03 126.98 -15.95 1.11e+00 8.12e-01 2.06e+02 angle pdb=" N VAL b 318 " pdb=" CA VAL b 318 " pdb=" CB VAL b 318 " ideal model delta sigma weight residual 112.28 97.93 14.35 1.00e+00 1.00e+00 2.06e+02 angle pdb=" CA HIS b 37 " pdb=" CB HIS b 37 " pdb=" CG HIS b 37 " ideal model delta sigma weight residual 113.80 99.70 14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" CA ALA b 273 " pdb=" C ALA b 273 " pdb=" N PRO b 274 " ideal model delta sigma weight residual 118.44 139.29 -20.85 1.59e+00 3.96e-01 1.72e+02 angle pdb=" CA PHE a1176 " pdb=" CB PHE a1176 " pdb=" CG PHE a1176 " ideal model delta sigma weight residual 113.80 101.01 12.79 1.00e+00 1.00e+00 1.64e+02 ... (remaining 27505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6123 17.92 - 35.84: 711 35.84 - 53.75: 257 53.75 - 71.67: 123 71.67 - 89.59: 26 Dihedral angle restraints: 7240 sinusoidal: 3915 harmonic: 3325 Sorted by residual: dihedral pdb=" CA THR a1119 " pdb=" C THR a1119 " pdb=" N GLY a1120 " pdb=" CA GLY a1120 " ideal model delta harmonic sigma weight residual -180.00 -98.21 -81.79 0 5.00e+00 4.00e-02 2.68e+02 dihedral pdb=" N THR b 240 " pdb=" C THR b 240 " pdb=" CA THR b 240 " pdb=" CB THR b 240 " ideal model delta harmonic sigma weight residual 123.40 150.45 -27.05 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N MET b 235 " pdb=" C MET b 235 " pdb=" CA MET b 235 " pdb=" CB MET b 235 " ideal model delta harmonic sigma weight residual 122.80 148.22 -25.42 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 7237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 819 0.243 - 0.486: 239 0.486 - 0.729: 84 0.729 - 0.972: 14 0.972 - 1.215: 3 Chirality restraints: 1159 Sorted by residual: chirality pdb=" CA MET b 235 " pdb=" N MET b 235 " pdb=" C MET b 235 " pdb=" CB MET b 235 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" CA THR b 240 " pdb=" N THR b 240 " pdb=" C THR b 240 " pdb=" CB THR b 240 " both_signs ideal model delta sigma weight residual False 2.53 1.35 1.18 2.00e-01 2.50e+01 3.47e+01 chirality pdb=" CA TYR a1159 " pdb=" N TYR a1159 " pdb=" C TYR a1159 " pdb=" CB TYR a1159 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 1156 not shown) Planarity restraints: 2314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a1024 " -0.478 2.00e-02 2.50e+03 2.01e-01 1.21e+03 pdb=" CG TYR a1024 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR a1024 " 0.166 2.00e-02 2.50e+03 pdb=" CD2 TYR a1024 " 0.159 2.00e-02 2.50e+03 pdb=" CE1 TYR a1024 " 0.112 2.00e-02 2.50e+03 pdb=" CE2 TYR a1024 " 0.123 2.00e-02 2.50e+03 pdb=" CZ TYR a1024 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR a1024 " -0.386 2.00e-02 2.50e+03 pdb=" HD1 TYR a1024 " 0.113 2.00e-02 2.50e+03 pdb=" HD2 TYR a1024 " 0.099 2.00e-02 2.50e+03 pdb=" HE1 TYR a1024 " 0.037 2.00e-02 2.50e+03 pdb=" HE2 TYR a1024 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 253 " -0.318 9.50e-02 1.11e+02 2.48e-01 1.14e+03 pdb=" NE ARG b 253 " -0.198 2.00e-02 2.50e+03 pdb=" CZ ARG b 253 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG b 253 " 0.150 2.00e-02 2.50e+03 pdb=" NH2 ARG b 253 " -0.040 2.00e-02 2.50e+03 pdb="HH11 ARG b 253 " -0.479 2.00e-02 2.50e+03 pdb="HH12 ARG b 253 " 0.359 2.00e-02 2.50e+03 pdb="HH21 ARG b 253 " 0.160 2.00e-02 2.50e+03 pdb="HH22 ARG b 253 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a1362 " 0.521 2.00e-02 2.50e+03 1.66e-01 1.10e+03 pdb=" CG TRP a1362 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP a1362 " -0.126 2.00e-02 2.50e+03 pdb=" CD2 TRP a1362 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP a1362 " -0.103 2.00e-02 2.50e+03 pdb=" CE2 TRP a1362 " -0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP a1362 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP a1362 " 0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP a1362 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP a1362 " 0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP a1362 " -0.192 2.00e-02 2.50e+03 pdb=" HE1 TRP a1362 " 0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP a1362 " -0.213 2.00e-02 2.50e+03 pdb=" HZ2 TRP a1362 " 0.105 2.00e-02 2.50e+03 pdb=" HZ3 TRP a1362 " -0.080 2.00e-02 2.50e+03 pdb=" HH2 TRP a1362 " 0.144 2.00e-02 2.50e+03 ... (remaining 2311 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 869 2.05 - 2.69: 23947 2.69 - 3.33: 43622 3.33 - 3.96: 58367 3.96 - 4.60: 88648 Nonbonded interactions: 215453 Sorted by model distance: nonbonded pdb=" H HIS M3175 " pdb=" H MET M3176 " model vdw 1.418 2.100 nonbonded pdb=" HG1 THR b 239 " pdb="HD21 LEU b 252 " model vdw 1.455 2.270 nonbonded pdb=" H ILE a1315 " pdb="HG22 ILE a1315 " model vdw 1.477 2.270 nonbonded pdb="HH22 ARG b 243 " pdb=" OD2 ASP b 251 " model vdw 1.496 2.450 nonbonded pdb=" OE2 GLU b 200 " pdb=" HH TYR b 202 " model vdw 1.496 2.450 ... (remaining 215448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.480 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: 0.260 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 39.550 Find NCS groups from input model: 0.130 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.035 0.159 7821 Z= 2.524 Angle : 3.740 20.852 10605 Z= 2.483 Chirality : 0.266 1.215 1159 Planarity : 0.041 0.330 1394 Dihedral : 19.808 89.588 2883 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 10.71 % Allowed : 18.61 % Favored : 70.69 % Rotamer: Outliers : 14.75 % Allowed : 14.27 % Favored : 70.98 % Cbeta Deviations : 16.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % Twisted General : 2.83 % 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: -6.77 (0.18), residues: 962 helix: -4.26 (0.14), residues: 444 sheet: -3.68 (0.42), residues: 121 loop : -4.93 (0.22), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.316 0.057 TRP a1362 HIS 0.018 0.005 HIS a1257 PHE 0.205 0.043 PHE a1112 TYR 0.421 0.063 TYR a1024 ARG 0.049 0.005 ARG a1079 Details of bonding type rmsd hydrogen bonds : bond 0.28191 ( 285) hydrogen bonds : angle 12.05327 ( 813) covalent geometry : bond 0.03452 ( 7821) covalent geometry : angle 3.73974 (10605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 126 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1003 GLU cc_start: 0.2677 (OUTLIER) cc_final: 0.0170 (mt-10) REVERT: a 1037 PRO cc_start: 0.8933 (OUTLIER) cc_final: 0.8685 (Cg_exo) REVERT: a 1038 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7636 (mtt90) REVERT: a 1063 PRO cc_start: 0.9187 (OUTLIER) cc_final: 0.8970 (Cg_exo) REVERT: a 1352 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8099 (mt) REVERT: b 162 PRO cc_start: 0.8934 (OUTLIER) cc_final: 0.8672 (Cg_endo) REVERT: b 292 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8022 (m) REVERT: b 301 MET cc_start: 0.7261 (mmp) cc_final: 0.6951 (mmp) REVERT: b 302 MET cc_start: 0.8424 (mtt) cc_final: 0.8128 (mtt) REVERT: b 325 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7384 (tmm) REVERT: b 343 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7446 (t80) REVERT: M 3095 MET cc_start: 0.0861 (ptt) cc_final: 0.0198 (ptt) REVERT: M 3134 LYS cc_start: 0.6337 (mttp) cc_final: 0.6116 (mttm) outliers start: 123 outliers final: 66 residues processed: 234 average time/residue: 0.4985 time to fit residues: 152.3773 Evaluate side-chains 177 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 102 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1003 GLU Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1015 GLN Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1036 VAL Chi-restraints excluded: chain a residue 1037 PRO Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1046 PRO Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1049 ILE Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1063 PRO Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1068 THR Chi-restraints excluded: chain a residue 1088 ILE Chi-restraints excluded: chain a residue 1125 SER Chi-restraints excluded: chain a residue 1152 SER Chi-restraints excluded: chain a residue 1158 PRO Chi-restraints excluded: chain a residue 1168 THR Chi-restraints excluded: chain a residue 1174 CYS Chi-restraints excluded: chain a residue 1179 ASP Chi-restraints excluded: chain a residue 1187 CYS Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1222 LEU Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1277 VAL Chi-restraints excluded: chain a residue 1323 THR Chi-restraints excluded: chain a residue 1326 LYS Chi-restraints excluded: chain a residue 1327 VAL Chi-restraints excluded: chain a residue 1334 PRO Chi-restraints excluded: chain a residue 1335 THR Chi-restraints excluded: chain a residue 1345 VAL Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1366 ASP Chi-restraints excluded: chain a residue 1376 ARG Chi-restraints excluded: chain a residue 1379 VAL Chi-restraints excluded: chain a residue 1402 LEU Chi-restraints excluded: chain a residue 1403 GLU Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 6 HIS Chi-restraints excluded: chain b residue 63 PRO Chi-restraints excluded: chain b residue 71 GLU Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 162 PRO Chi-restraints excluded: chain b residue 164 ARG Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 251 ASP Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 292 THR Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 343 PHE Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 404 PHE Chi-restraints excluded: chain b residue 419 THR Chi-restraints excluded: chain b residue 428 LEU Chi-restraints excluded: chain M residue 3114 ASN Chi-restraints excluded: chain M residue 3115 ILE Chi-restraints excluded: chain M residue 3119 GLN Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3141 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1008 HIS a1102 GLN a1166 HIS a1180 ASN a1274 ASN ** b 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 300 ASN b 331 GLN ** b 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 337 ASN M3216 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.096768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.075943 restraints weight = 62911.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.078497 restraints weight = 28431.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.080161 restraints weight = 17600.445| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 7821 Z= 0.279 Angle : 1.042 11.326 10605 Z= 0.557 Chirality : 0.049 0.187 1159 Planarity : 0.011 0.138 1394 Dihedral : 14.376 87.081 1208 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 1.46 % Allowed : 15.28 % Favored : 83.26 % Rotamer: Outliers : 10.19 % Allowed : 18.11 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.65 % 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: -5.53 (0.21), residues: 962 helix: -3.20 (0.18), residues: 445 sheet: -3.39 (0.44), residues: 120 loop : -4.23 (0.23), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP b 407 HIS 0.015 0.002 HIS b 28 PHE 0.021 0.003 PHE b 169 TYR 0.020 0.003 TYR b 435 ARG 0.007 0.001 ARG b 308 Details of bonding type rmsd hydrogen bonds : bond 0.07335 ( 285) hydrogen bonds : angle 7.30968 ( 813) covalent geometry : bond 0.00613 ( 7821) covalent geometry : angle 1.04161 (10605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 112 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1024 TYR cc_start: 0.8017 (m-80) cc_final: 0.7574 (m-10) REVERT: a 1038 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6198 (mtm-85) REVERT: a 1166 HIS cc_start: 0.8659 (OUTLIER) cc_final: 0.8312 (t70) REVERT: a 1352 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7935 (mt) REVERT: a 1406 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.6621 (t80) REVERT: b 83 PHE cc_start: 0.6867 (OUTLIER) cc_final: 0.6094 (t80) REVERT: b 302 MET cc_start: 0.8907 (mtt) cc_final: 0.8691 (mtt) REVERT: b 323 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8136 (pmm) REVERT: b 325 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7309 (tmm) REVERT: b 404 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.6984 (t80) REVERT: b 415 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7812 (pp20) REVERT: b 420 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: M 3095 MET cc_start: -0.1099 (ptt) cc_final: -0.1485 (ptt) REVERT: M 3118 GLN cc_start: 0.8699 (pm20) cc_final: 0.8331 (mp10) REVERT: M 3183 TYR cc_start: 0.8913 (m-10) cc_final: 0.8671 (m-10) outliers start: 85 outliers final: 53 residues processed: 184 average time/residue: 0.5793 time to fit residues: 139.5535 Evaluate side-chains 166 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 103 time to evaluate : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1166 HIS Chi-restraints excluded: chain a residue 1168 THR Chi-restraints excluded: chain a residue 1174 CYS Chi-restraints excluded: chain a residue 1187 CYS Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1200 ASN Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1277 VAL Chi-restraints excluded: chain a residue 1300 LYS Chi-restraints excluded: chain a residue 1323 THR Chi-restraints excluded: chain a residue 1326 LYS Chi-restraints excluded: chain a residue 1345 VAL Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1366 ASP Chi-restraints excluded: chain a residue 1376 ARG Chi-restraints excluded: chain a residue 1379 VAL Chi-restraints excluded: chain a residue 1403 GLU Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain a residue 1409 VAL Chi-restraints excluded: chain b residue 6 HIS Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 145 THR Chi-restraints excluded: chain b residue 164 ARG Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 251 ASP Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 294 GLN Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 404 PHE Chi-restraints excluded: chain b residue 415 GLU Chi-restraints excluded: chain b residue 419 THR Chi-restraints excluded: chain b residue 420 GLU Chi-restraints excluded: chain M residue 3110 ARG Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3141 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN b 28 HIS b 50 ASN b 136 GLN b 294 GLN b 336 GLN b 406 HIS M3109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.097443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.076396 restraints weight = 61975.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.078992 restraints weight = 27725.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.080708 restraints weight = 17068.312| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7821 Z= 0.222 Angle : 0.825 9.394 10605 Z= 0.441 Chirality : 0.045 0.163 1159 Planarity : 0.007 0.115 1394 Dihedral : 12.346 96.733 1144 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 1.04 % Allowed : 13.62 % Favored : 85.34 % Rotamer: Outliers : 8.87 % Allowed : 18.35 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -4.67 (0.23), residues: 962 helix: -2.29 (0.20), residues: 449 sheet: -3.26 (0.41), residues: 142 loop : -3.93 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M3151 HIS 0.006 0.001 HIS a1166 PHE 0.014 0.002 PHE M3188 TYR 0.019 0.002 TYR a1198 ARG 0.004 0.001 ARG a1282 Details of bonding type rmsd hydrogen bonds : bond 0.05730 ( 285) hydrogen bonds : angle 6.37621 ( 813) covalent geometry : bond 0.00474 ( 7821) covalent geometry : angle 0.82469 (10605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 113 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1065 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.6808 (pm20) REVERT: a 1198 TYR cc_start: 0.4060 (OUTLIER) cc_final: 0.1802 (m-80) REVERT: a 1352 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8054 (mt) REVERT: a 1406 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.6936 (t80) REVERT: b 83 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6426 (t80) REVERT: b 149 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7905 (tpp) REVERT: b 302 MET cc_start: 0.8920 (mtt) cc_final: 0.8635 (mtt) REVERT: b 323 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8035 (pmm) REVERT: b 415 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8008 (pp20) REVERT: M 3095 MET cc_start: -0.1134 (ptt) cc_final: -0.1525 (ptt) REVERT: M 3116 LYS cc_start: 0.8558 (tppt) cc_final: 0.8338 (tppt) REVERT: M 3118 GLN cc_start: 0.8769 (pm20) cc_final: 0.8327 (mp10) REVERT: M 3119 GLN cc_start: 0.8745 (pt0) cc_final: 0.8524 (pt0) REVERT: M 3134 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7538 (mttm) REVERT: M 3138 GLU cc_start: 0.7595 (mp0) cc_final: 0.7373 (tp30) REVERT: M 3152 ARG cc_start: 0.6982 (tpp-160) cc_final: 0.6445 (tpp-160) outliers start: 74 outliers final: 48 residues processed: 174 average time/residue: 0.5439 time to fit residues: 128.2421 Evaluate side-chains 158 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 102 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1089 ILE Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1166 HIS Chi-restraints excluded: chain a residue 1174 CYS Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1200 ASN Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1216 LEU Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1274 ASN Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1326 LYS Chi-restraints excluded: chain a residue 1345 VAL Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1376 ARG Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain a residue 1409 VAL Chi-restraints excluded: chain b residue 6 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 215 ARG Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 251 ASP Chi-restraints excluded: chain b residue 252 LEU Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 415 GLU Chi-restraints excluded: chain b residue 419 THR Chi-restraints excluded: chain M residue 3110 ARG Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3141 CYS Chi-restraints excluded: chain M residue 3153 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1166 HIS a1274 ASN b 50 ASN M3155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.097219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.077766 restraints weight = 62366.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080107 restraints weight = 28100.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.081715 restraints weight = 17422.427| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 7821 Z= 0.254 Angle : 0.780 8.929 10605 Z= 0.413 Chirality : 0.044 0.163 1159 Planarity : 0.006 0.076 1394 Dihedral : 11.040 88.176 1118 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.73 % Allowed : 13.72 % Favored : 85.55 % Rotamer: Outliers : 8.03 % Allowed : 18.11 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -4.23 (0.24), residues: 962 helix: -1.80 (0.22), residues: 448 sheet: -3.19 (0.43), residues: 128 loop : -3.83 (0.26), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a1021 HIS 0.009 0.001 HIS b 406 PHE 0.017 0.002 PHE a1369 TYR 0.022 0.002 TYR a1198 ARG 0.005 0.001 ARG a1282 Details of bonding type rmsd hydrogen bonds : bond 0.05284 ( 285) hydrogen bonds : angle 6.06005 ( 813) covalent geometry : bond 0.00548 ( 7821) covalent geometry : angle 0.77956 (10605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 107 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 1003 GLU cc_start: 0.1694 (OUTLIER) cc_final: 0.0589 (mt-10) REVERT: a 1038 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.6508 (mtt90) REVERT: a 1128 MET cc_start: 0.8697 (mmt) cc_final: 0.8464 (mmt) REVERT: a 1198 TYR cc_start: 0.3758 (OUTLIER) cc_final: 0.1431 (m-80) REVERT: a 1274 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7295 (t0) REVERT: a 1352 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8451 (mt) REVERT: a 1406 TYR cc_start: 0.8796 (OUTLIER) cc_final: 0.6855 (t80) REVERT: b 83 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6471 (t80) REVERT: b 149 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7925 (tpp) REVERT: b 215 ARG cc_start: 0.8613 (ptm160) cc_final: 0.8329 (ptm160) REVERT: b 295 MET cc_start: 0.7952 (mtp) cc_final: 0.7747 (ttm) REVERT: b 302 MET cc_start: 0.8976 (mtt) cc_final: 0.8634 (mtt) REVERT: b 323 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8115 (pmm) REVERT: b 415 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8025 (pp20) REVERT: M 3095 MET cc_start: -0.1036 (ptt) cc_final: -0.1474 (ptt) REVERT: M 3134 LYS cc_start: 0.7833 (ttmm) cc_final: 0.7408 (mttp) REVERT: M 3138 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: M 3152 ARG cc_start: 0.7088 (tpp-160) cc_final: 0.6649 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8103 (tt0) cc_final: 0.7186 (tp-100) outliers start: 67 outliers final: 48 residues processed: 163 average time/residue: 0.5392 time to fit residues: 116.0581 Evaluate side-chains 161 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 102 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1003 GLU Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1089 ILE Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1166 HIS Chi-restraints excluded: chain a residue 1174 CYS Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1200 ASN Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1274 ASN Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1345 VAL Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 6 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 44 LEU Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 113 GLU Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 194 LEU Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 251 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 415 GLU Chi-restraints excluded: chain b residue 419 THR Chi-restraints excluded: chain M residue 3106 LEU Chi-restraints excluded: chain M residue 3110 ARG Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3126 MET Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3138 GLU Chi-restraints excluded: chain M residue 3141 CYS Chi-restraints excluded: chain M residue 3155 GLN Chi-restraints excluded: chain M residue 3214 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 90 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN a1346 GLN b 50 ASN b 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.099534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079430 restraints weight = 61526.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.081887 restraints weight = 27490.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.083619 restraints weight = 16774.535| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7821 Z= 0.135 Angle : 0.683 6.797 10605 Z= 0.355 Chirality : 0.042 0.136 1159 Planarity : 0.006 0.078 1394 Dihedral : 10.105 89.325 1101 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.98 % Favored : 89.29 % Rotamer: Outliers : 6.12 % Allowed : 18.71 % Favored : 75.18 % 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: -3.71 (0.25), residues: 962 helix: -1.30 (0.23), residues: 448 sheet: -3.17 (0.42), residues: 128 loop : -3.59 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M3151 HIS 0.016 0.001 HIS a1166 PHE 0.009 0.001 PHE M3219 TYR 0.015 0.001 TYR M3170 ARG 0.003 0.000 ARG a1396 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 285) hydrogen bonds : angle 5.56336 ( 813) covalent geometry : bond 0.00297 ( 7821) covalent geometry : angle 0.68302 (10605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 106 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1038 ARG cc_start: 0.7324 (OUTLIER) cc_final: 0.6362 (mtt90) REVERT: a 1088 ILE cc_start: 0.8768 (tp) cc_final: 0.8541 (tp) REVERT: a 1198 TYR cc_start: 0.3935 (OUTLIER) cc_final: 0.1701 (m-80) REVERT: a 1274 ASN cc_start: 0.6960 (OUTLIER) cc_final: 0.6537 (t0) REVERT: a 1352 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8373 (mt) REVERT: a 1406 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.6821 (t80) REVERT: b 83 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6744 (t80) REVERT: b 149 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7879 (tpp) REVERT: b 217 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7919 (mp) REVERT: b 235 MET cc_start: 0.7686 (ptm) cc_final: 0.6973 (ptm) REVERT: b 295 MET cc_start: 0.8018 (mtp) cc_final: 0.7740 (ttm) REVERT: b 302 MET cc_start: 0.8930 (mtt) cc_final: 0.8632 (mtt) REVERT: b 323 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8056 (pmm) REVERT: b 415 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7932 (pp20) REVERT: M 3095 MET cc_start: -0.0875 (ptt) cc_final: -0.1320 (ptt) REVERT: M 3118 GLN cc_start: 0.8647 (pm20) cc_final: 0.8237 (mp10) REVERT: M 3134 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7517 (mttm) REVERT: M 3138 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7364 (tp30) REVERT: M 3150 ASN cc_start: 0.7615 (t0) cc_final: 0.6625 (p0) REVERT: M 3152 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.6489 (tpp-160) REVERT: M 3156 GLN cc_start: 0.7986 (tt0) cc_final: 0.7027 (tp-100) outliers start: 51 outliers final: 32 residues processed: 149 average time/residue: 0.5459 time to fit residues: 105.7621 Evaluate side-chains 143 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1274 ASN Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1345 VAL Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 6 HIS Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 217 LEU Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 251 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 415 GLU Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3138 GLU Chi-restraints excluded: chain M residue 3141 CYS Chi-restraints excluded: chain M residue 3144 LEU Chi-restraints excluded: chain M residue 3193 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 92 optimal weight: 20.0000 chunk 91 optimal weight: 30.0000 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN b 50 ASN b 334 ASN b 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.097556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.076415 restraints weight = 62299.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.078995 restraints weight = 27376.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.080759 restraints weight = 16640.001| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7821 Z= 0.198 Angle : 0.694 7.549 10605 Z= 0.362 Chirality : 0.043 0.144 1159 Planarity : 0.006 0.077 1394 Dihedral : 9.842 85.503 1098 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.27 % Favored : 87.11 % Rotamer: Outliers : 6.59 % Allowed : 18.71 % Favored : 74.70 % 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: -3.66 (0.24), residues: 962 helix: -1.27 (0.23), residues: 445 sheet: -3.19 (0.42), residues: 128 loop : -3.50 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a1021 HIS 0.006 0.001 HIS b 406 PHE 0.012 0.002 PHE a1369 TYR 0.018 0.002 TYR a1198 ARG 0.003 0.000 ARG M3124 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 285) hydrogen bonds : angle 5.56523 ( 813) covalent geometry : bond 0.00433 ( 7821) covalent geometry : angle 0.69447 (10605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1038 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6350 (mtt90) REVERT: a 1128 MET cc_start: 0.8687 (mmt) cc_final: 0.8403 (mmt) REVERT: a 1198 TYR cc_start: 0.3652 (OUTLIER) cc_final: 0.1384 (m-80) REVERT: a 1352 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8415 (mt) REVERT: a 1406 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.6827 (t80) REVERT: b 83 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.6599 (t80) REVERT: b 149 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8064 (tpp) REVERT: b 235 MET cc_start: 0.7704 (ptm) cc_final: 0.6978 (ptm) REVERT: b 295 MET cc_start: 0.7986 (mtp) cc_final: 0.7697 (ttm) REVERT: b 302 MET cc_start: 0.8889 (mtt) cc_final: 0.8473 (mtt) REVERT: M 3095 MET cc_start: -0.0906 (ptt) cc_final: -0.1338 (ptt) REVERT: M 3134 LYS cc_start: 0.7923 (ttmm) cc_final: 0.7488 (mttm) REVERT: M 3138 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: M 3150 ASN cc_start: 0.7734 (t0) cc_final: 0.6837 (p0) REVERT: M 3152 ARG cc_start: 0.7042 (tpp-160) cc_final: 0.6558 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8020 (tt0) cc_final: 0.7066 (tp-100) REVERT: M 3212 TRP cc_start: 0.7868 (t60) cc_final: 0.7655 (t60) outliers start: 55 outliers final: 39 residues processed: 150 average time/residue: 0.6524 time to fit residues: 129.2611 Evaluate side-chains 145 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1089 ILE Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1287 MET Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 6 HIS Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain b residue 236 SER Chi-restraints excluded: chain b residue 251 ASP Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain M residue 3106 LEU Chi-restraints excluded: chain M residue 3110 ARG Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3138 GLU Chi-restraints excluded: chain M residue 3141 CYS Chi-restraints excluded: chain M residue 3144 LEU Chi-restraints excluded: chain M residue 3193 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN b 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.097850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.077098 restraints weight = 61853.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.079774 restraints weight = 26608.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.081528 restraints weight = 16117.035| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7821 Z= 0.160 Angle : 0.659 6.827 10605 Z= 0.342 Chirality : 0.042 0.134 1159 Planarity : 0.006 0.077 1394 Dihedral : 9.520 84.812 1095 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.43 % Favored : 88.05 % Rotamer: Outliers : 6.00 % Allowed : 19.30 % Favored : 74.70 % 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: -3.43 (0.25), residues: 962 helix: -1.04 (0.23), residues: 450 sheet: -3.15 (0.43), residues: 128 loop : -3.44 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a1021 HIS 0.004 0.001 HIS b 406 PHE 0.009 0.001 PHE a1369 TYR 0.022 0.001 TYR b 312 ARG 0.008 0.000 ARG b 311 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 285) hydrogen bonds : angle 5.43027 ( 813) covalent geometry : bond 0.00353 ( 7821) covalent geometry : angle 0.65895 (10605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 103 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1038 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6215 (mtt90) REVERT: a 1198 TYR cc_start: 0.3883 (OUTLIER) cc_final: 0.1707 (m-80) REVERT: a 1341 ASP cc_start: 0.7632 (m-30) cc_final: 0.7288 (m-30) REVERT: a 1352 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8354 (mt) REVERT: a 1406 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.6878 (t80) REVERT: b 83 PHE cc_start: 0.7243 (OUTLIER) cc_final: 0.6610 (t80) REVERT: b 127 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: b 149 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8077 (tpp) REVERT: b 235 MET cc_start: 0.7627 (ptm) cc_final: 0.6862 (ptm) REVERT: b 302 MET cc_start: 0.8888 (mtt) cc_final: 0.8511 (mtt) REVERT: b 323 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8070 (pmm) REVERT: M 3095 MET cc_start: -0.0811 (ptt) cc_final: -0.1277 (ptt) REVERT: M 3134 LYS cc_start: 0.7935 (ttmm) cc_final: 0.7540 (mttm) REVERT: M 3138 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7391 (tp30) REVERT: M 3150 ASN cc_start: 0.7683 (t0) cc_final: 0.6766 (p0) REVERT: M 3152 ARG cc_start: 0.7211 (tpp-160) cc_final: 0.6752 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8059 (tt0) cc_final: 0.7115 (tp-100) REVERT: M 3212 TRP cc_start: 0.7958 (t60) cc_final: 0.7677 (t60) outliers start: 50 outliers final: 35 residues processed: 146 average time/residue: 0.5608 time to fit residues: 107.2331 Evaluate side-chains 143 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 99 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1089 ILE Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1287 MET Chi-restraints excluded: chain a residue 1326 LYS Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 207 GLU Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 236 SER Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain M residue 3106 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3138 GLU Chi-restraints excluded: chain M residue 3141 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN b 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.098504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.078688 restraints weight = 60522.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.080873 restraints weight = 27330.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.082424 restraints weight = 16963.124| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7821 Z= 0.162 Angle : 0.651 6.904 10605 Z= 0.338 Chirality : 0.042 0.134 1159 Planarity : 0.006 0.078 1394 Dihedral : 9.216 83.663 1090 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.54 % Favored : 87.94 % Rotamer: Outliers : 5.76 % Allowed : 20.02 % Favored : 74.22 % 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: -3.22 (0.25), residues: 962 helix: -0.86 (0.24), residues: 450 sheet: -2.95 (0.45), residues: 128 loop : -3.38 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a1021 HIS 0.005 0.001 HIS b 406 PHE 0.016 0.001 PHE b 377 TYR 0.016 0.001 TYR b 312 ARG 0.011 0.001 ARG b 311 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 285) hydrogen bonds : angle 5.32925 ( 813) covalent geometry : bond 0.00358 ( 7821) covalent geometry : angle 0.65126 (10605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1038 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6274 (mtt90) REVERT: a 1198 TYR cc_start: 0.4038 (OUTLIER) cc_final: 0.1769 (m-80) REVERT: a 1341 ASP cc_start: 0.7575 (m-30) cc_final: 0.7259 (m-30) REVERT: a 1352 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8424 (mt) REVERT: a 1406 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.6857 (t80) REVERT: b 83 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6690 (t80) REVERT: b 127 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6536 (mp0) REVERT: b 149 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8031 (tpp) REVERT: b 235 MET cc_start: 0.7617 (ptm) cc_final: 0.6873 (ptm) REVERT: b 302 MET cc_start: 0.8898 (mtt) cc_final: 0.8462 (mtt) REVERT: b 323 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.8067 (pmm) REVERT: b 425 MET cc_start: 0.8098 (tmm) cc_final: 0.7866 (tmm) REVERT: M 3095 MET cc_start: -0.0608 (ptt) cc_final: -0.1042 (ptt) REVERT: M 3150 ASN cc_start: 0.7683 (t0) cc_final: 0.6774 (p0) REVERT: M 3152 ARG cc_start: 0.7280 (tpp-160) cc_final: 0.6816 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8112 (tt0) cc_final: 0.7144 (tp-100) REVERT: M 3212 TRP cc_start: 0.7947 (t60) cc_final: 0.7497 (t60) outliers start: 48 outliers final: 39 residues processed: 138 average time/residue: 0.6632 time to fit residues: 123.4030 Evaluate side-chains 146 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 99 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1089 ILE Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1274 ASN Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1287 MET Chi-restraints excluded: chain a residue 1326 LYS Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 207 GLU Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 236 SER Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 432 TYR Chi-restraints excluded: chain M residue 3106 LEU Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3133 VAL Chi-restraints excluded: chain M residue 3141 CYS Chi-restraints excluded: chain M residue 3214 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.4980 chunk 69 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN b 50 ASN ** b 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.099014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.079235 restraints weight = 60569.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081494 restraints weight = 27313.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.083138 restraints weight = 16837.555| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7821 Z= 0.147 Angle : 0.644 6.637 10605 Z= 0.332 Chirality : 0.041 0.137 1159 Planarity : 0.006 0.078 1394 Dihedral : 9.051 83.066 1089 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.19 % Favored : 89.29 % Rotamer: Outliers : 5.52 % Allowed : 20.86 % Favored : 73.62 % 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: -3.04 (0.26), residues: 962 helix: -0.69 (0.24), residues: 446 sheet: -2.90 (0.45), residues: 128 loop : -3.28 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP a1021 HIS 0.004 0.001 HIS b 406 PHE 0.008 0.001 PHE M3219 TYR 0.015 0.001 TYR b 312 ARG 0.010 0.000 ARG b 311 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 285) hydrogen bonds : angle 5.21519 ( 813) covalent geometry : bond 0.00327 ( 7821) covalent geometry : angle 0.64446 (10605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 98 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1038 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6069 (mtt90) REVERT: a 1198 TYR cc_start: 0.3840 (OUTLIER) cc_final: 0.1661 (m-80) REVERT: a 1208 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8067 (tt) REVERT: a 1274 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7945 (m-40) REVERT: a 1341 ASP cc_start: 0.7583 (m-30) cc_final: 0.7270 (m-30) REVERT: a 1352 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8406 (mt) REVERT: a 1406 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.6808 (t80) REVERT: b 83 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6676 (t80) REVERT: b 127 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: b 149 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.8052 (tpp) REVERT: b 235 MET cc_start: 0.7606 (ptm) cc_final: 0.6793 (ptm) REVERT: b 302 MET cc_start: 0.8845 (mtt) cc_final: 0.8454 (mtt) REVERT: b 323 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8076 (pmm) REVERT: b 398 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7513 (mmt) REVERT: b 425 MET cc_start: 0.8079 (tmm) cc_final: 0.7815 (tmm) REVERT: M 3095 MET cc_start: -0.0620 (ptt) cc_final: -0.1037 (ptt) REVERT: M 3152 ARG cc_start: 0.7205 (tpp-160) cc_final: 0.6833 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8102 (tt0) cc_final: 0.7125 (tp-100) REVERT: M 3212 TRP cc_start: 0.7938 (t60) cc_final: 0.7409 (t60) outliers start: 46 outliers final: 35 residues processed: 137 average time/residue: 0.6031 time to fit residues: 109.9111 Evaluate side-chains 142 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 96 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1089 ILE Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1274 ASN Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1287 MET Chi-restraints excluded: chain a residue 1326 LYS Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 207 GLU Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 217 LEU Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 236 SER Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 432 TYR Chi-restraints excluded: chain M residue 3106 LEU Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3141 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN b 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.097391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.076196 restraints weight = 61538.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.078613 restraints weight = 27058.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080371 restraints weight = 16683.409| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.6586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7821 Z= 0.215 Angle : 0.684 7.296 10605 Z= 0.356 Chirality : 0.043 0.137 1159 Planarity : 0.006 0.076 1394 Dihedral : 9.092 83.539 1089 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.95 % Favored : 87.53 % Rotamer: Outliers : 6.00 % Allowed : 20.50 % Favored : 73.50 % 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: -3.19 (0.25), residues: 962 helix: -0.82 (0.24), residues: 447 sheet: -3.03 (0.45), residues: 128 loop : -3.33 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a1021 HIS 0.007 0.001 HIS b 406 PHE 0.013 0.002 PHE a1369 TYR 0.019 0.002 TYR a1198 ARG 0.010 0.001 ARG b 311 Details of bonding type rmsd hydrogen bonds : bond 0.04289 ( 285) hydrogen bonds : angle 5.35582 ( 813) covalent geometry : bond 0.00471 ( 7821) covalent geometry : angle 0.68372 (10605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 97 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 1038 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6042 (mtt90) REVERT: a 1198 TYR cc_start: 0.3410 (OUTLIER) cc_final: 0.1136 (m-80) REVERT: a 1341 ASP cc_start: 0.7621 (m-30) cc_final: 0.7321 (m-30) REVERT: a 1352 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8297 (mt) REVERT: a 1406 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.6863 (t80) REVERT: b 83 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6725 (t80) REVERT: b 127 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6583 (mp0) REVERT: b 149 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8122 (tpp) REVERT: b 186 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.6980 (t0) REVERT: b 235 MET cc_start: 0.7690 (ptm) cc_final: 0.6874 (ptm) REVERT: b 302 MET cc_start: 0.8821 (mtt) cc_final: 0.8433 (mtt) REVERT: b 323 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8085 (pmm) REVERT: b 398 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7386 (mmt) REVERT: b 425 MET cc_start: 0.8133 (tmm) cc_final: 0.7830 (tmm) REVERT: M 3095 MET cc_start: -0.0452 (ptt) cc_final: -0.0888 (ptt) REVERT: M 3134 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7517 (mttm) REVERT: M 3152 ARG cc_start: 0.7218 (tpp-160) cc_final: 0.6800 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8026 (tt0) cc_final: 0.6977 (tp-100) REVERT: M 3183 TYR cc_start: 0.8711 (m-10) cc_final: 0.8505 (m-10) REVERT: M 3212 TRP cc_start: 0.8038 (t60) cc_final: 0.7557 (t60) outliers start: 50 outliers final: 38 residues processed: 138 average time/residue: 0.6548 time to fit residues: 122.2342 Evaluate side-chains 143 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1009 VAL Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1020 CYS Chi-restraints excluded: chain a residue 1021 TRP Chi-restraints excluded: chain a residue 1038 ARG Chi-restraints excluded: chain a residue 1040 VAL Chi-restraints excluded: chain a residue 1047 THR Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1089 ILE Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1197 THR Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1208 ILE Chi-restraints excluded: chain a residue 1234 VAL Chi-restraints excluded: chain a residue 1279 CYS Chi-restraints excluded: chain a residue 1287 MET Chi-restraints excluded: chain a residue 1326 LYS Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1362 TRP Chi-restraints excluded: chain a residue 1406 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 49 ILE Chi-restraints excluded: chain b residue 83 PHE Chi-restraints excluded: chain b residue 113 GLU Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 127 GLU Chi-restraints excluded: chain b residue 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 186 ASN Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 207 GLU Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 217 LEU Chi-restraints excluded: chain b residue 230 LEU Chi-restraints excluded: chain b residue 236 SER Chi-restraints excluded: chain b residue 255 LEU Chi-restraints excluded: chain b residue 259 MET Chi-restraints excluded: chain b residue 290 GLU Chi-restraints excluded: chain b residue 323 MET Chi-restraints excluded: chain b residue 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 432 TYR Chi-restraints excluded: chain M residue 3106 LEU Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3141 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 88 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 90 optimal weight: 40.0000 chunk 27 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.097260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.076058 restraints weight = 61523.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.078386 restraints weight = 27369.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.080069 restraints weight = 16798.176| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 7821 Z= 0.266 Angle : 0.990 59.194 10605 Z= 0.591 Chirality : 0.046 0.594 1159 Planarity : 0.006 0.076 1394 Dihedral : 9.105 83.597 1089 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.06 % Favored : 87.42 % Rotamer: Outliers : 5.64 % Allowed : 20.74 % Favored : 73.62 % Cbeta Deviations : 0.11 % 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: -3.22 (0.25), residues: 962 helix: -0.85 (0.24), residues: 447 sheet: -3.04 (0.45), residues: 128 loop : -3.33 (0.28), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a1021 HIS 0.007 0.001 HIS b 406 PHE 0.014 0.002 PHE a1369 TYR 0.033 0.002 TYR M3210 ARG 0.007 0.001 ARG b 311 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 285) hydrogen bonds : angle 5.37359 ( 813) covalent geometry : bond 0.00564 ( 7821) covalent geometry : angle 0.98968 (10605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6213.51 seconds wall clock time: 113 minutes 2.21 seconds (6782.21 seconds total)