Starting phenix.real_space_refine on Thu Sep 18 06:49:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiq_9997/09_2025/6kiq_9997.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiq_9997/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kiq_9997/09_2025/6kiq_9997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiq_9997/09_2025/6kiq_9997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kiq_9997/09_2025/6kiq_9997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiq_9997/09_2025/6kiq_9997.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.31, per 1000 atoms: 0.22 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: 1.51 Conformation dependent library (CDL) restraints added in 693.7 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.42 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: 3.92 Time building geometry restraints manager: 2.13 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: 0.560 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: 0.110 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.450 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.360 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.049 0.005 ARG a1079 TYR 0.421 0.063 TYR a1024 PHE 0.205 0.043 PHE a1112 TRP 0.316 0.057 TRP a1362 HIS 0.018 0.005 HIS a1257 Details of bonding type rmsd covalent geometry : bond 0.03452 ( 7821) covalent geometry : angle 3.73974 (10605) hydrogen bonds : bond 0.28191 ( 285) hydrogen bonds : angle 12.05327 ( 813) *********************** 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 : 0.438 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: symmetry clash revert: symmetry clash REVERT: a 1003 GLU cc_start: 0.2677 (OUTLIER) cc_final: 0.0165 (mt-10) REVERT: a 1037 PRO cc_start: 0.8933 (OUTLIER) cc_final: 0.8684 (Cg_exo) REVERT: a 1038 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7635 (mtt90) REVERT: a 1063 PRO cc_start: 0.9187 (OUTLIER) cc_final: 0.8967 (Cg_exo) REVERT: a 1352 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8105 (mt) REVERT: b 162 PRO cc_start: 0.8934 (OUTLIER) cc_final: 0.8670 (Cg_endo) REVERT: b 292 THR cc_start: 0.8453 (OUTLIER) cc_final: 0.8021 (m) REVERT: b 301 MET cc_start: 0.7261 (mmp) cc_final: 0.6941 (mmp) REVERT: b 302 MET cc_start: 0.8424 (mtt) cc_final: 0.8117 (mtt) REVERT: b 325 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7378 (tmm) REVERT: b 343 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7444 (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: 0.6111 (mttm) outliers start: 123 outliers final: 67 residues processed: 234 average time/residue: 0.2404 time to fit residues: 73.2937 Evaluate side-chains 179 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 103 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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 352 LYS 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 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 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 37 HIS b 300 ASN b 331 GLN b 336 GLN b 337 ASN M3216 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.096624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.075823 restraints weight = 63085.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.078371 restraints weight = 28390.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.080050 restraints weight = 17617.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081001 restraints weight = 13260.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.081397 restraints weight = 11331.674| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 7821 Z= 0.289 Angle : 1.038 11.501 10605 Z= 0.557 Chirality : 0.050 0.192 1159 Planarity : 0.011 0.137 1394 Dihedral : 14.457 86.164 1212 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 1.46 % Allowed : 15.38 % Favored : 83.16 % Rotamer: Outliers : 10.19 % Allowed : 18.35 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.54 (0.21), residues: 962 helix: -3.21 (0.18), residues: 445 sheet: -3.35 (0.44), residues: 120 loop : -4.26 (0.23), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 390 TYR 0.019 0.003 TYR b 435 PHE 0.019 0.003 PHE b 169 TRP 0.030 0.003 TRP b 407 HIS 0.014 0.002 HIS b 28 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 7821) covalent geometry : angle 1.03827 (10605) hydrogen bonds : bond 0.07496 ( 285) hydrogen bonds : angle 7.37268 ( 813) *********************** 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 : 0.292 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: a 1024 TYR cc_start: 0.7981 (m-80) cc_final: 0.7564 (m-10) REVERT: a 1038 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6325 (mtt90) REVERT: a 1166 HIS cc_start: 0.8648 (OUTLIER) cc_final: 0.8301 (t70) REVERT: a 1352 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7935 (mt) REVERT: a 1406 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.6674 (t80) REVERT: b 83 PHE cc_start: 0.6831 (OUTLIER) cc_final: 0.6113 (t80) REVERT: b 302 MET cc_start: 0.8932 (mtt) cc_final: 0.8625 (mtt) REVERT: b 323 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.8135 (pmm) REVERT: b 325 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7309 (tmm) REVERT: b 344 VAL cc_start: 0.7455 (OUTLIER) cc_final: 0.6498 (t) REVERT: b 404 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7019 (t80) REVERT: b 415 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.7805 (pp20) REVERT: b 420 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: M 3095 MET cc_start: -0.1202 (ptt) cc_final: -0.1589 (ptt) REVERT: M 3118 GLN cc_start: 0.8669 (pm20) cc_final: 0.8255 (mp10) REVERT: M 3146 TYR cc_start: 0.7887 (m-80) cc_final: 0.7440 (m-80) outliers start: 85 outliers final: 51 residues processed: 185 average time/residue: 0.2377 time to fit residues: 56.6502 Evaluate side-chains 165 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 103 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 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 323 MET Chi-restraints excluded: chain b residue 325 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 344 VAL 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 59 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 M3109 GLN M3119 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.099292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.078065 restraints weight = 61142.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.080693 restraints weight = 27155.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.082428 restraints weight = 16520.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.083538 restraints weight = 12355.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.083983 restraints weight = 10408.310| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 7821 Z= 0.162 Angle : 0.787 8.569 10605 Z= 0.419 Chirality : 0.044 0.169 1159 Planarity : 0.007 0.113 1394 Dihedral : 12.087 99.749 1144 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 1.04 % Allowed : 11.23 % Favored : 87.73 % Rotamer: Outliers : 7.55 % Allowed : 18.47 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.23), residues: 962 helix: -1.98 (0.21), residues: 444 sheet: -3.05 (0.43), residues: 137 loop : -3.83 (0.26), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M3152 TYR 0.021 0.002 TYR a1146 PHE 0.017 0.002 PHE M3188 TRP 0.017 0.002 TRP M3151 HIS 0.006 0.001 HIS a1166 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7821) covalent geometry : angle 0.78737 (10605) hydrogen bonds : bond 0.05425 ( 285) hydrogen bonds : angle 6.11526 ( 813) *********************** 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 181 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 118 time to evaluate : 0.310 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 1198 TYR cc_start: 0.3558 (OUTLIER) cc_final: 0.1555 (m-80) REVERT: a 1352 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7923 (mt) REVERT: a 1406 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.6831 (t80) REVERT: b 83 PHE cc_start: 0.7141 (OUTLIER) cc_final: 0.6360 (t80) REVERT: b 149 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7827 (tpp) REVERT: b 301 MET cc_start: 0.7526 (mmp) cc_final: 0.7290 (mmp) REVERT: b 302 MET cc_start: 0.8929 (mtt) cc_final: 0.8607 (mtt) REVERT: b 323 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.8065 (pmm) REVERT: b 415 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: M 3095 MET cc_start: -0.1080 (ptt) cc_final: -0.1476 (ptt) REVERT: M 3114 ASN cc_start: 0.8172 (t0) cc_final: 0.7912 (t0) REVERT: M 3116 LYS cc_start: 0.8408 (tppt) cc_final: 0.8203 (tppt) REVERT: M 3118 GLN cc_start: 0.8750 (pm20) cc_final: 0.8312 (mp10) REVERT: M 3119 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8360 (pt0) REVERT: M 3134 LYS cc_start: 0.7955 (ttmm) cc_final: 0.7551 (mttm) REVERT: M 3138 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: M 3146 TYR cc_start: 0.7812 (m-80) cc_final: 0.7310 (m-80) REVERT: M 3152 ARG cc_start: 0.6976 (tpp-160) cc_final: 0.6455 (tpp-160) REVERT: M 3183 TYR cc_start: 0.8914 (m-10) cc_final: 0.8689 (m-10) outliers start: 63 outliers final: 38 residues processed: 167 average time/residue: 0.2367 time to fit residues: 51.4446 Evaluate side-chains 155 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 108 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 1062 HIS 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 1279 CYS 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 b residue 6 HIS 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 164 ARG 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 326 LYS 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 3119 GLN Chi-restraints excluded: chain M residue 3120 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 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 39 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 40.0000 chunk 69 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1166 HIS a1274 ASN ** b 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 37 HIS b 136 GLN b 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.097863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.076596 restraints weight = 62180.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.079182 restraints weight = 28111.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.080965 restraints weight = 17473.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.081965 restraints weight = 13154.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.082554 restraints weight = 11211.183| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7821 Z= 0.204 Angle : 0.740 8.415 10605 Z= 0.389 Chirality : 0.043 0.149 1159 Planarity : 0.006 0.078 1394 Dihedral : 10.769 86.067 1116 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.95 % Favored : 87.32 % Rotamer: Outliers : 6.71 % Allowed : 19.30 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.04 (0.24), residues: 962 helix: -1.71 (0.22), residues: 450 sheet: -2.95 (0.43), residues: 132 loop : -3.72 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a1282 TYR 0.018 0.002 TYR a1198 PHE 0.013 0.002 PHE M3188 TRP 0.017 0.002 TRP a1021 HIS 0.004 0.001 HIS a1166 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 7821) covalent geometry : angle 0.73966 (10605) hydrogen bonds : bond 0.05035 ( 285) hydrogen bonds : angle 5.83839 ( 813) *********************** 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 165 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 109 time to evaluate : 0.432 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 1128 MET cc_start: 0.8706 (mmt) cc_final: 0.8489 (mmt) REVERT: a 1198 TYR cc_start: 0.3931 (OUTLIER) cc_final: 0.1736 (m-80) REVERT: a 1352 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8210 (mt) REVERT: a 1406 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.6785 (t80) REVERT: b 83 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.6883 (t80) REVERT: b 149 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7919 (tpp) REVERT: b 211 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8555 (m-30) REVERT: b 215 ARG cc_start: 0.8618 (ptm160) cc_final: 0.8341 (ptm160) REVERT: b 302 MET cc_start: 0.8964 (mtt) cc_final: 0.8660 (mtt) REVERT: b 415 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7998 (pp20) REVERT: M 3095 MET cc_start: -0.1175 (ptt) cc_final: -0.1582 (ptt) REVERT: M 3114 ASN cc_start: 0.8303 (t0) cc_final: 0.8057 (t0) REVERT: M 3116 LYS cc_start: 0.8394 (tppt) cc_final: 0.8084 (tppt) REVERT: M 3118 GLN cc_start: 0.8702 (pm20) cc_final: 0.8200 (mp10) REVERT: M 3119 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7919 (pt0) REVERT: M 3134 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7535 (mttm) REVERT: M 3146 TYR cc_start: 0.7838 (m-80) cc_final: 0.7374 (m-80) REVERT: M 3152 ARG cc_start: 0.6948 (tpp-160) cc_final: 0.6473 (tpp-160) REVERT: M 3156 GLN cc_start: 0.7892 (tt0) cc_final: 0.6879 (tp-100) REVERT: M 3183 TYR cc_start: 0.8895 (m-10) cc_final: 0.8678 (m-10) REVERT: M 3203 SER cc_start: 0.6788 (t) cc_final: 0.6370 (t) REVERT: M 3206 CYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7509 (m) outliers start: 56 outliers final: 39 residues processed: 155 average time/residue: 0.2614 time to fit residues: 52.4498 Evaluate side-chains 152 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 104 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 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 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 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 195 VAL Chi-restraints excluded: chain b residue 211 ASP 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 347 ILE Chi-restraints excluded: chain b residue 398 MET Chi-restraints excluded: chain b residue 415 GLU Chi-restraints excluded: chain M residue 3110 ARG Chi-restraints excluded: chain M residue 3119 GLN Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3206 CYS 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 43 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.097238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.076261 restraints weight = 62459.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.078863 restraints weight = 27355.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.080589 restraints weight = 16845.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.081637 restraints weight = 12679.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.082223 restraints weight = 10752.961| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5766 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= 0.217 Angle : 0.721 7.605 10605 Z= 0.380 Chirality : 0.043 0.147 1159 Planarity : 0.006 0.078 1394 Dihedral : 10.052 89.505 1096 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.27 % Favored : 87.11 % Rotamer: Outliers : 7.55 % Allowed : 17.39 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.81 (0.24), residues: 962 helix: -1.47 (0.23), residues: 446 sheet: -3.10 (0.43), residues: 128 loop : -3.54 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M3181 TYR 0.018 0.002 TYR a1198 PHE 0.014 0.002 PHE a1369 TRP 0.017 0.002 TRP a1021 HIS 0.007 0.001 HIS b 406 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 7821) covalent geometry : angle 0.72099 (10605) hydrogen bonds : bond 0.04871 ( 285) hydrogen bonds : angle 5.71484 ( 813) *********************** 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 171 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 108 time to evaluate : 0.428 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: a 1038 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6450 (mtt90) REVERT: a 1198 TYR cc_start: 0.3719 (OUTLIER) cc_final: 0.1406 (m-80) REVERT: a 1274 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7390 (t0) REVERT: a 1276 MET cc_start: 0.8055 (mtt) cc_final: 0.7833 (mtp) REVERT: a 1352 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8334 (mt) REVERT: a 1406 TYR cc_start: 0.8669 (OUTLIER) cc_final: 0.6823 (t80) REVERT: b 75 MET cc_start: 0.7641 (mtt) cc_final: 0.7408 (mtt) REVERT: b 83 PHE cc_start: 0.7265 (OUTLIER) cc_final: 0.6524 (t80) REVERT: b 149 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7901 (tpp) REVERT: b 215 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8332 (ptm160) REVERT: b 235 MET cc_start: 0.7885 (ptm) cc_final: 0.7045 (ptm) REVERT: b 301 MET cc_start: 0.7353 (mmp) cc_final: 0.7073 (mmp) REVERT: b 302 MET cc_start: 0.8930 (mtt) cc_final: 0.8596 (mtt) REVERT: b 415 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7980 (pp20) REVERT: M 3095 MET cc_start: -0.1043 (ptt) cc_final: -0.1491 (ptt) REVERT: M 3109 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8702 (mm-40) REVERT: M 3114 ASN cc_start: 0.8289 (t0) cc_final: 0.8015 (t0) REVERT: M 3119 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: M 3134 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7656 (mttm) REVERT: M 3146 TYR cc_start: 0.7815 (m-80) cc_final: 0.7341 (m-80) REVERT: M 3152 ARG cc_start: 0.7074 (tpp-160) cc_final: 0.6602 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8019 (tt0) cc_final: 0.7047 (tp-100) REVERT: M 3183 TYR cc_start: 0.8896 (m-10) cc_final: 0.8683 (m-10) REVERT: M 3203 SER cc_start: 0.6859 (t) cc_final: 0.6429 (t) REVERT: M 3206 CYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7451 (m) outliers start: 63 outliers final: 43 residues processed: 160 average time/residue: 0.2467 time to fit residues: 51.4912 Evaluate side-chains 158 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 104 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 1174 CYS 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 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 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 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 b residue 415 GLU Chi-restraints excluded: chain M residue 3106 LEU Chi-restraints excluded: chain M residue 3110 ARG Chi-restraints excluded: chain M residue 3113 LYS Chi-restraints excluded: chain M residue 3119 GLN 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 3206 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN a1346 GLN 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 = 0.3974 r_free = 0.3974 target = 0.098782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.077919 restraints weight = 61385.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.080652 restraints weight = 26553.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.082403 restraints weight = 16120.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.083450 restraints weight = 12028.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.084056 restraints weight = 10184.141| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7821 Z= 0.135 Angle : 0.654 6.803 10605 Z= 0.338 Chirality : 0.041 0.136 1159 Planarity : 0.005 0.078 1394 Dihedral : 9.593 87.840 1096 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.50 % Favored : 88.98 % Rotamer: Outliers : 6.71 % Allowed : 18.35 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.25), residues: 962 helix: -1.10 (0.23), residues: 459 sheet: -2.94 (0.45), residues: 123 loop : -3.50 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M3181 TYR 0.021 0.001 TYR M3170 PHE 0.009 0.001 PHE M3219 TRP 0.015 0.002 TRP a1021 HIS 0.004 0.001 HIS a1283 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7821) covalent geometry : angle 0.65368 (10605) hydrogen bonds : bond 0.04356 ( 285) hydrogen bonds : angle 5.40926 ( 813) *********************** 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 162 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 106 time to evaluate : 0.431 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: 0.7355 (OUTLIER) cc_final: 0.6281 (mtt90) REVERT: a 1198 TYR cc_start: 0.3691 (OUTLIER) cc_final: 0.1531 (m-80) REVERT: a 1274 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.5870 (t0) REVERT: a 1276 MET cc_start: 0.7771 (mtt) cc_final: 0.7528 (mtp) REVERT: a 1352 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8344 (mt) REVERT: a 1406 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.6816 (t80) REVERT: b 83 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.6808 (t80) REVERT: b 149 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: b 235 MET cc_start: 0.7611 (ptm) cc_final: 0.6878 (ptm) REVERT: b 301 MET cc_start: 0.7343 (mmp) cc_final: 0.6996 (mmp) REVERT: b 302 MET cc_start: 0.8892 (mtt) cc_final: 0.8575 (mtt) REVERT: b 323 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8029 (pmm) REVERT: M 3095 MET cc_start: -0.1127 (ptt) cc_final: -0.1555 (ptt) REVERT: M 3116 LYS cc_start: 0.8401 (tppt) cc_final: 0.8145 (tppt) REVERT: M 3118 GLN cc_start: 0.8603 (pm20) cc_final: 0.8164 (mp10) REVERT: M 3119 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7975 (pt0) REVERT: M 3124 ARG cc_start: 0.8620 (tmm-80) cc_final: 0.7670 (tmt-80) REVERT: M 3134 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7675 (mttm) REVERT: M 3146 TYR cc_start: 0.7754 (m-80) cc_final: 0.7380 (m-80) REVERT: M 3150 ASN cc_start: 0.7797 (t0) cc_final: 0.6776 (p0) REVERT: M 3152 ARG cc_start: 0.7058 (tpp-160) cc_final: 0.6585 (tpp-160) REVERT: M 3156 GLN cc_start: 0.8004 (tt0) cc_final: 0.7008 (tp-100) REVERT: M 3183 TYR cc_start: 0.8882 (m-10) cc_final: 0.8626 (m-10) REVERT: M 3203 SER cc_start: 0.6741 (t) cc_final: 0.6311 (t) REVERT: M 3206 CYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7411 (m) outliers start: 56 outliers final: 37 residues processed: 153 average time/residue: 0.2475 time to fit residues: 48.8018 Evaluate side-chains 147 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 1183 ILE 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 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 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 207 GLU Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 230 LEU 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 311 ARG 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 3113 LYS Chi-restraints excluded: chain M residue 3119 GLN Chi-restraints excluded: chain M residue 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3144 LEU Chi-restraints excluded: chain M residue 3206 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 27 optimal weight: 7.9990 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN ** a1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 186 ASN b 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.098352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.077178 restraints weight = 61219.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.079900 restraints weight = 26886.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.081674 restraints weight = 16422.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.082718 restraints weight = 12306.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.083131 restraints weight = 10437.466| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6261 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= 0.165 Angle : 0.655 6.807 10605 Z= 0.341 Chirality : 0.042 0.134 1159 Planarity : 0.005 0.076 1394 Dihedral : 9.483 88.615 1093 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.23 % Favored : 88.25 % Rotamer: Outliers : 5.76 % Allowed : 19.18 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.25), residues: 962 helix: -1.02 (0.23), residues: 460 sheet: -2.87 (0.46), residues: 123 loop : -3.51 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M3110 TYR 0.015 0.001 TYR a1198 PHE 0.010 0.001 PHE b 377 TRP 0.016 0.002 TRP a1021 HIS 0.005 0.001 HIS b 406 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7821) covalent geometry : angle 0.65543 (10605) hydrogen bonds : bond 0.04319 ( 285) hydrogen bonds : angle 5.44176 ( 813) *********************** 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 150 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.435 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 1038 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6224 (mtt90) REVERT: a 1128 MET cc_start: 0.8676 (mmt) cc_final: 0.8403 (mmt) REVERT: a 1198 TYR cc_start: 0.3804 (OUTLIER) cc_final: 0.1639 (m-80) REVERT: a 1274 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6442 (t0) REVERT: a 1276 MET cc_start: 0.7881 (mtt) cc_final: 0.7676 (mtp) REVERT: a 1352 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8406 (mt) REVERT: a 1406 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.6905 (t80) REVERT: b 83 PHE cc_start: 0.7235 (OUTLIER) cc_final: 0.6642 (t80) REVERT: b 149 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8034 (tpp) REVERT: b 186 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.6897 (t0) REVERT: b 235 MET cc_start: 0.7636 (ptm) cc_final: 0.6876 (ptm) REVERT: b 301 MET cc_start: 0.7468 (mmp) cc_final: 0.7070 (mmp) REVERT: b 302 MET cc_start: 0.8884 (mtt) cc_final: 0.8504 (mtt) REVERT: b 323 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8042 (pmm) REVERT: M 3095 MET cc_start: -0.0899 (ptt) cc_final: -0.1345 (ptt) REVERT: M 3124 ARG cc_start: 0.8603 (tmm-80) cc_final: 0.7582 (ttm110) REVERT: M 3134 LYS cc_start: 0.8263 (ttmm) cc_final: 0.7683 (mttm) REVERT: M 3146 TYR cc_start: 0.7857 (m-80) cc_final: 0.7444 (m-80) REVERT: M 3152 ARG cc_start: 0.7082 (tpp-160) cc_final: 0.6555 (tpp-160) REVERT: M 3179 GLN cc_start: 0.8912 (mp10) cc_final: 0.8642 (pm20) REVERT: M 3203 SER cc_start: 0.6793 (t) cc_final: 0.6366 (t) REVERT: M 3206 CYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7450 (m) REVERT: M 3212 TRP cc_start: 0.7956 (t60) cc_final: 0.7724 (t60) outliers start: 48 outliers final: 35 residues processed: 142 average time/residue: 0.2530 time to fit residues: 46.2721 Evaluate side-chains 142 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 1183 ILE 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 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 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 214 PHE Chi-restraints excluded: chain b residue 230 LEU 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 311 ARG 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 3120 LEU Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3141 CYS Chi-restraints excluded: chain M residue 3206 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 57 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 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 ** a1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 186 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.097915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.076919 restraints weight = 61393.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.079501 restraints weight = 26883.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.081267 restraints weight = 16286.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.082309 restraints weight = 12147.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.082886 restraints weight = 10288.762| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.6329 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= 0.194 Angle : 0.667 7.111 10605 Z= 0.348 Chirality : 0.042 0.134 1159 Planarity : 0.006 0.075 1394 Dihedral : 9.397 84.734 1091 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.06 % Favored : 87.42 % Rotamer: Outliers : 6.00 % Allowed : 19.06 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.25), residues: 962 helix: -0.95 (0.23), residues: 453 sheet: -2.87 (0.46), residues: 123 loop : -3.41 (0.27), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M3181 TYR 0.017 0.002 TYR a1198 PHE 0.013 0.002 PHE a1369 TRP 0.017 0.002 TRP a1021 HIS 0.006 0.001 HIS b 406 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7821) covalent geometry : angle 0.66670 (10605) hydrogen bonds : bond 0.04409 ( 285) hydrogen bonds : angle 5.42572 ( 813) *********************** 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 149 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 0.434 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 1038 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6430 (mtt90) REVERT: a 1198 TYR cc_start: 0.3471 (OUTLIER) cc_final: 0.1211 (m-80) REVERT: a 1274 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6653 (t0) REVERT: a 1341 ASP cc_start: 0.7579 (m-30) cc_final: 0.7254 (m-30) REVERT: a 1352 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8327 (mt) REVERT: a 1406 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.6894 (t80) REVERT: b 83 PHE cc_start: 0.7164 (OUTLIER) cc_final: 0.6579 (t80) REVERT: b 149 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8062 (tpp) REVERT: b 186 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7542 (t0) REVERT: b 207 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8368 (pm20) REVERT: b 235 MET cc_start: 0.7658 (ptm) cc_final: 0.6897 (ptm) REVERT: b 301 MET cc_start: 0.7501 (mmp) cc_final: 0.7038 (mmp) REVERT: b 302 MET cc_start: 0.8853 (mtt) cc_final: 0.8459 (mtt) REVERT: b 323 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8076 (pmm) REVERT: M 3095 MET cc_start: -0.0839 (ptt) cc_final: -0.1301 (ptt) REVERT: M 3118 GLN cc_start: 0.8635 (pm20) cc_final: 0.8259 (mp10) REVERT: M 3124 ARG cc_start: 0.8610 (tmm-80) cc_final: 0.7603 (ttm110) REVERT: M 3134 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7552 (mttm) REVERT: M 3146 TYR cc_start: 0.7780 (m-80) cc_final: 0.7467 (m-80) REVERT: M 3152 ARG cc_start: 0.7020 (tpp-160) cc_final: 0.6537 (tpp-160) REVERT: M 3166 ASN cc_start: 0.9487 (t0) cc_final: 0.9267 (t0) REVERT: M 3179 GLN cc_start: 0.8982 (mp10) cc_final: 0.8690 (pm20) REVERT: M 3203 SER cc_start: 0.6938 (t) cc_final: 0.6530 (t) REVERT: M 3206 CYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7546 (m) REVERT: M 3212 TRP cc_start: 0.8032 (t60) cc_final: 0.7717 (t60) outliers start: 50 outliers final: 38 residues processed: 143 average time/residue: 0.2576 time to fit residues: 47.5355 Evaluate side-chains 146 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 97 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 1183 ILE 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 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 139 HIS Chi-restraints excluded: chain b residue 149 MET Chi-restraints excluded: chain b residue 174 SER 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 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 311 ARG 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 3131 SER Chi-restraints excluded: chain M residue 3141 CYS Chi-restraints excluded: chain M residue 3206 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 7 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3988 r_free = 0.3988 target = 0.099538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.078329 restraints weight = 60246.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.081085 restraints weight = 26439.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.082876 restraints weight = 16098.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.083897 restraints weight = 12058.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.084547 restraints weight = 10261.047| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7821 Z= 0.118 Angle : 0.628 7.059 10605 Z= 0.324 Chirality : 0.041 0.141 1159 Planarity : 0.005 0.076 1394 Dihedral : 9.015 85.797 1089 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.56 % Favored : 89.92 % Rotamer: Outliers : 5.04 % Allowed : 20.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.97 (0.26), residues: 962 helix: -0.68 (0.24), residues: 460 sheet: -2.72 (0.47), residues: 123 loop : -3.34 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG b 320 TYR 0.012 0.001 TYR b 312 PHE 0.007 0.001 PHE b 377 TRP 0.014 0.002 TRP a1021 HIS 0.005 0.001 HIS a1283 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7821) covalent geometry : angle 0.62847 (10605) hydrogen bonds : bond 0.04067 ( 285) hydrogen bonds : angle 5.19141 ( 813) *********************** 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: 42 poor density : 102 time to evaluate : 0.330 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 1198 TYR cc_start: 0.3703 (OUTLIER) cc_final: 0.1563 (m-80) REVERT: a 1341 ASP cc_start: 0.7558 (m-30) cc_final: 0.7254 (m-30) REVERT: a 1352 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8321 (mt) REVERT: a 1406 TYR cc_start: 0.8574 (OUTLIER) cc_final: 0.6801 (t80) REVERT: b 83 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6764 (t80) REVERT: b 149 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8028 (tpp) REVERT: b 207 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: b 235 MET cc_start: 0.7590 (ptm) cc_final: 0.6813 (ptm) REVERT: b 302 MET cc_start: 0.8808 (mtt) cc_final: 0.8361 (mtt) REVERT: b 323 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8088 (pmm) REVERT: b 398 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7487 (mmt) REVERT: b 425 MET cc_start: 0.8007 (tmm) cc_final: 0.7756 (tmm) REVERT: M 3095 MET cc_start: -0.0826 (ptt) cc_final: -0.1292 (ptt) REVERT: M 3118 GLN cc_start: 0.8620 (pm20) cc_final: 0.8238 (mp10) REVERT: M 3124 ARG cc_start: 0.8592 (tmm-80) cc_final: 0.7599 (ttm110) REVERT: M 3134 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7520 (mttm) REVERT: M 3146 TYR cc_start: 0.7783 (m-80) cc_final: 0.7463 (m-80) REVERT: M 3152 ARG cc_start: 0.6783 (tpp-160) cc_final: 0.6407 (tpp-160) REVERT: M 3166 ASN cc_start: 0.9492 (t0) cc_final: 0.9279 (t0) REVERT: M 3179 GLN cc_start: 0.8918 (mp10) cc_final: 0.8651 (pm20) REVERT: M 3212 TRP cc_start: 0.8072 (t60) cc_final: 0.7612 (t60) outliers start: 42 outliers final: 27 residues processed: 138 average time/residue: 0.2655 time to fit residues: 47.1453 Evaluate side-chains 135 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 1089 ILE 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 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 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 186 ASN 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 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 398 MET Chi-restraints excluded: chain b residue 432 TYR Chi-restraints excluded: chain M residue 3106 LEU 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 48 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 90 optimal weight: 50.0000 chunk 57 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3984 r_free = 0.3984 target = 0.099277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.078328 restraints weight = 60488.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.081020 restraints weight = 26472.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.082770 restraints weight = 16084.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.083826 restraints weight = 12048.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.084257 restraints weight = 10205.257| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.6636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7821 Z= 0.135 Angle : 0.624 6.723 10605 Z= 0.320 Chirality : 0.041 0.134 1159 Planarity : 0.005 0.076 1394 Dihedral : 8.581 83.815 1085 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.52 % Allowed : 10.50 % Favored : 88.98 % Rotamer: Outliers : 4.32 % Allowed : 21.22 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.83 (0.26), residues: 962 helix: -0.59 (0.24), residues: 457 sheet: -2.67 (0.47), residues: 123 loop : -3.20 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M3110 TYR 0.014 0.001 TYR b 312 PHE 0.021 0.001 PHE M3219 TRP 0.015 0.002 TRP a1021 HIS 0.005 0.001 HIS a1283 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7821) covalent geometry : angle 0.62413 (10605) hydrogen bonds : bond 0.03956 ( 285) hydrogen bonds : angle 5.15014 ( 813) ********************** 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 138 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.468 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 1198 TYR cc_start: 0.3722 (OUTLIER) cc_final: 0.1600 (m-80) REVERT: a 1341 ASP cc_start: 0.7584 (m-30) cc_final: 0.7263 (m-30) REVERT: a 1352 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8342 (mt) REVERT: a 1406 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.6847 (t80) REVERT: b 83 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6783 (t80) REVERT: b 149 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8026 (tpp) REVERT: b 207 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8310 (pm20) REVERT: b 235 MET cc_start: 0.7527 (ptm) cc_final: 0.6693 (ptm) REVERT: b 302 MET cc_start: 0.8752 (mtt) cc_final: 0.8377 (mtt) REVERT: b 323 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8161 (pmm) REVERT: b 398 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7377 (mmt) REVERT: b 425 MET cc_start: 0.8037 (tmm) cc_final: 0.7751 (tmm) REVERT: M 3095 MET cc_start: -0.0698 (ptt) cc_final: -0.1165 (ptt) REVERT: M 3124 ARG cc_start: 0.8599 (tmm-80) cc_final: 0.7686 (tmt-80) REVERT: M 3134 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7495 (mttm) REVERT: M 3146 TYR cc_start: 0.7831 (m-80) cc_final: 0.7487 (m-80) REVERT: M 3152 ARG cc_start: 0.6814 (tpp-160) cc_final: 0.6424 (tpp-160) REVERT: M 3166 ASN cc_start: 0.9487 (t0) cc_final: 0.9235 (t0) REVERT: M 3179 GLN cc_start: 0.8890 (mp10) cc_final: 0.8601 (pm20) REVERT: M 3184 MET cc_start: 0.8100 (mmp) cc_final: 0.7890 (mmp) REVERT: M 3219 PHE cc_start: 0.8214 (t80) cc_final: 0.8000 (t80) outliers start: 36 outliers final: 26 residues processed: 132 average time/residue: 0.2593 time to fit residues: 44.3775 Evaluate side-chains 132 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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 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 1089 ILE 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 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 207 GLU Chi-restraints excluded: chain b residue 214 PHE Chi-restraints excluded: chain b residue 230 LEU 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 398 MET Chi-restraints excluded: chain b residue 432 TYR Chi-restraints excluded: chain M residue 3106 LEU 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 86 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 93 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN ** a1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 293 GLN b 385 GLN ** M3214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.096904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.076109 restraints weight = 61296.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.078517 restraints weight = 26973.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.080272 restraints weight = 16738.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.081322 restraints weight = 12496.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.081872 restraints weight = 10588.656| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.6617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7821 Z= 0.244 Angle : 0.700 7.761 10605 Z= 0.366 Chirality : 0.044 0.150 1159 Planarity : 0.006 0.073 1394 Dihedral : 8.815 85.727 1085 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.79 % Favored : 86.69 % Rotamer: Outliers : 5.16 % Allowed : 20.86 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.26), residues: 962 helix: -0.80 (0.24), residues: 448 sheet: -2.93 (0.46), residues: 123 loop : -3.22 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a1347 TYR 0.021 0.002 TYR a1024 PHE 0.022 0.002 PHE M3219 TRP 0.021 0.002 TRP a1021 HIS 0.008 0.001 HIS b 406 Details of bonding type rmsd covalent geometry : bond 0.00538 ( 7821) covalent geometry : angle 0.70008 (10605) hydrogen bonds : bond 0.04402 ( 285) hydrogen bonds : angle 5.45132 ( 813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3137.74 seconds wall clock time: 54 minutes 11.32 seconds (3251.32 seconds total)