Starting phenix.real_space_refine on Fri Jun 13 10:38:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kio_9996/06_2025/6kio_9996.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kio_9996/06_2025/6kio_9996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kio_9996/06_2025/6kio_9996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kio_9996/06_2025/6kio_9996.map" model { file = "/net/cci-nas-00/data/ceres_data/6kio_9996/06_2025/6kio_9996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kio_9996/06_2025/6kio_9996.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.015 sd= 0.059 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 7442 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 95 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15091 Number of models: 1 Model: "" Number of chains: 3 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: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2132 Classifications: {'peptide': 130} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} 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} Time building chain proxies: 7.11, per 1000 atoms: 0.47 Number of scatterers: 15091 At special positions: 0 Unit cell: (81.84, 108.24, 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 7442 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS M3101 " - pdb=" SG CYS M3222 " distance=1.97 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: 3.99 Conformation dependent library (CDL) restraints added in 1.0 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 56.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'b' and resid 10 through 27 removed outlier: 3.632A pdb=" N GLY b 17 " --> pdb=" O GLY b 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS b 19 " --> pdb=" O GLN b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 48 removed outlier: 4.035A pdb=" N LEU b 44 " --> pdb=" O SER b 40 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG b 48 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 53 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 102 through 108 Processing helix chain 'b' and resid 110 through 115 Processing helix chain 'b' and resid 115 through 127 removed outlier: 4.707A pdb=" N VAL b 121 " --> pdb=" O SER b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 161 removed outlier: 4.142A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY b 148 " --> pdb=" O GLY b 144 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET b 149 " --> pdb=" O THR b 145 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N SER b 155 " --> pdb=" O THR b 151 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS b 156 " --> pdb=" O LEU b 152 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU b 159 " --> pdb=" O SER b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 195 removed outlier: 3.513A pdb=" N ASN b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER b 190 " --> pdb=" O ASN b 186 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS b 192 " --> pdb=" O THR b 188 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN b 193 " --> pdb=" O LEU b 189 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 216 removed outlier: 3.768A pdb=" N CYS b 213 " --> pdb=" O LEU b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 223 through 239 removed outlier: 3.578A pdb=" N LEU b 227 " --> pdb=" O THR b 223 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR b 234 " --> pdb=" O LEU b 230 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR b 239 " --> pdb=" O MET b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 240 through 244 Processing helix chain 'b' and resid 251 through 258 Processing helix chain 'b' and resid 278 through 282 Processing helix chain 'b' and resid 288 through 296 Processing helix chain 'b' and resid 297 through 301 Processing helix chain 'b' and resid 306 through 310 Processing helix chain 'b' and resid 324 through 339 removed outlier: 3.592A pdb=" N GLN b 331 " --> pdb=" O GLU b 327 " (cutoff:3.500A) Processing helix chain 'b' and resid 340 through 343 Processing helix chain 'b' and resid 384 through 400 removed outlier: 4.055A pdb=" N PHE b 388 " --> pdb=" O ILE b 384 " (cutoff:3.500A) removed outlier: 5.050A 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 414 through 435 removed outlier: 4.218A pdb=" N PHE b 418 " --> pdb=" O ASP b 414 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL b 429 " --> pdb=" O MET b 425 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) Processing helix chain 'M' and resid 3101 through 3113 removed outlier: 3.518A pdb=" N ILE M3105 " --> pdb=" O CYS M3101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN M3109 " --> pdb=" O ILE M3105 " (cutoff:3.500A) Processing helix chain 'M' and resid 3116 through 3126 removed outlier: 3.850A pdb=" N MET M3126 " --> pdb=" O GLU M3122 " (cutoff:3.500A) Processing helix chain 'M' and resid 3130 through 3145 removed outlier: 3.987A pdb=" N VAL M3136 " --> pdb=" O GLY M3132 " (cutoff:3.500A) Processing helix chain 'M' and resid 3150 through 3160 removed outlier: 3.653A pdb=" N LYS M3160 " --> pdb=" O GLN M3156 " (cutoff:3.500A) Processing helix chain 'M' and resid 3162 through 3170 removed outlier: 3.612A pdb=" N ILE M3167 " --> pdb=" O PHE M3163 " (cutoff:3.500A) Processing helix chain 'M' and resid 3179 through 3188 removed outlier: 3.517A pdb=" N TYR M3183 " --> pdb=" O GLN M3179 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU M3185 " --> pdb=" O ARG M3181 " (cutoff:3.500A) Processing helix chain 'M' and resid 3195 through 3203 Processing helix chain 'M' and resid 3206 through 3219 Processing helix chain 'a' and resid 1010 through 1029 removed outlier: 4.070A pdb=" N GLN a1015 " --> pdb=" O GLN a1011 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU a1022 " --> pdb=" O ASN a1018 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS a1028 " --> pdb=" O TYR a1024 " (cutoff:3.500A) Processing helix chain 'a' and resid 1046 through 1055 removed outlier: 3.906A pdb=" N GLU a1051 " --> pdb=" O THR a1047 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL a1052 " --> pdb=" O VAL a1048 " (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: 3.549A pdb=" N GLY a1080 " --> pdb=" O ASN a1076 " (cutoff:3.500A) Processing helix chain 'a' and resid 1082 through 1103 removed outlier: 4.476A pdb=" N GLU a1087 " --> pdb=" O THR a1083 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE a1088 " --> pdb=" O ILE a1084 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP a1090 " --> pdb=" O LYS a1086 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU a1091 " --> pdb=" O GLU a1087 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN a1102 " --> pdb=" O LYS a1098 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS a1103 " --> pdb=" O LEU a1099 " (cutoff:3.500A) Processing helix chain 'a' and resid 1117 through 1135 removed outlier: 4.217A pdb=" N SER a1121 " --> pdb=" O GLY a1117 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY a1122 " --> pdb=" O GLY a1118 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR a1124 " --> pdb=" O GLY a1120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU a1126 " --> pdb=" O GLY a1122 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL a1133 " --> pdb=" O GLU a1129 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP a1134 " --> pdb=" O ARG a1130 " (cutoff:3.500A) Processing helix chain 'a' and resid 1156 through 1170 removed outlier: 4.112A pdb=" N THR a1164 " --> pdb=" O ASN a1160 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS a1166 " --> pdb=" O ILE a1162 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR a1167 " --> pdb=" O LEU a1163 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU a1170 " --> pdb=" O HIS a1166 " (cutoff:3.500A) Processing helix chain 'a' and resid 1179 through 1190 removed outlier: 3.722A pdb=" N ASP a1185 " --> pdb=" O GLU a1181 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE a1186 " --> pdb=" O ALA a1182 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS a1187 " --> pdb=" O ILE a1183 " (cutoff:3.500A) Processing helix chain 'a' and resid 1197 through 1217 removed outlier: 3.865A pdb=" N ARG a1203 " --> pdb=" O THR a1199 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN a1207 " --> pdb=" O ARG a1203 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER a1210 " --> pdb=" O GLY a1206 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE a1212 " --> pdb=" O ILE a1208 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR a1213 " --> pdb=" O VAL a1209 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA a1214 " --> pdb=" O SER a1210 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER a1215 " --> pdb=" O SER a1211 " (cutoff:3.500A) Processing helix chain 'a' and resid 1225 through 1234 Processing helix chain 'a' and resid 1261 through 1268 Processing helix chain 'a' and resid 1269 through 1270 No H-bonds generated for 'chain 'a' and resid 1269 through 1270' Processing helix chain 'a' and resid 1271 through 1275 Processing helix chain 'a' and resid 1280 through 1284 removed outlier: 3.775A pdb=" N HIS a1283 " --> pdb=" O ASP a1280 " (cutoff:3.500A) Processing helix chain 'a' and resid 1298 through 1311 removed outlier: 3.928A pdb=" N VAL a1302 " --> pdb=" O VAL a1298 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ALA a1307 " --> pdb=" O ASN a1303 " (cutoff:3.500A) Processing helix chain 'a' and resid 1358 through 1375 removed outlier: 3.515A pdb=" N ARG a1364 " --> pdb=" O GLU a1360 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU a1365 " --> pdb=" O ALA a1361 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS a1368 " --> pdb=" O ARG a1364 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE a1369 " --> pdb=" O LEU a1365 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET a1372 " --> pdb=" O LYS a1368 " (cutoff:3.500A) Processing helix chain 'a' and resid 1379 through 1384 Processing helix chain 'a' and resid 1388 through 1404 removed outlier: 3.683A pdb=" N ASP a1398 " --> pdb=" O GLU a1394 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET a1399 " --> pdb=" O ALA a1395 " (cutoff:3.500A) Processing helix chain 'a' and resid 1404 through 1409 Processing sheet with id=AA1, first strand: chain 'b' and resid 92 through 94 removed outlier: 7.684A pdb=" N VAL b 93 " --> pdb=" O ALA b 65 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU b 67 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL b 68 " --> pdb=" O GLN b 8 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL b 5 " --> pdb=" O GLN b 136 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR b 138 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE b 7 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER b 140 " --> pdb=" O ILE b 7 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ALA b 9 " --> pdb=" O SER b 140 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE b 135 " --> pdb=" O ASN b 167 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE b 169 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU b 137 " --> pdb=" O PHE b 169 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL b 171 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N HIS b 139 " --> pdb=" O VAL b 171 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET b 166 " --> pdb=" O GLU b 200 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR b 202 " --> pdb=" O MET b 166 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR b 168 " --> pdb=" O TYR b 202 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR b 201 " --> pdb=" O PHE b 268 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N CYS b 203 " --> pdb=" O PRO b 270 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE b 267 " --> pdb=" O SER b 381 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER b 381 " --> pdb=" O PHE b 267 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY b 379 " --> pdb=" O MET b 269 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N THR b 314 " --> pdb=" O ASN b 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 92 through 94 removed outlier: 7.684A pdb=" N VAL b 93 " --> pdb=" O ALA b 65 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU b 67 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL b 68 " --> pdb=" O GLN b 8 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL b 5 " --> pdb=" O GLN b 136 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR b 138 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE b 7 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N SER b 140 " --> pdb=" O ILE b 7 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ALA b 9 " --> pdb=" O SER b 140 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N PHE b 135 " --> pdb=" O ASN b 167 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE b 169 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU b 137 " --> pdb=" O PHE b 169 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL b 171 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N HIS b 139 " --> pdb=" O VAL b 171 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N MET b 166 " --> pdb=" O GLU b 200 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR b 202 " --> pdb=" O MET b 166 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR b 168 " --> pdb=" O TYR b 202 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N THR b 201 " --> pdb=" O PHE b 268 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N CYS b 203 " --> pdb=" O PRO b 270 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE b 267 " --> pdb=" O SER b 381 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N SER b 381 " --> pdb=" O PHE b 267 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY b 379 " --> pdb=" O MET b 269 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER b 374 " --> pdb=" O ARG b 320 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N PHE b 319 " --> pdb=" O CYS b 356 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 1066 through 1068 removed outlier: 7.931A pdb=" N ILE a1067 " --> pdb=" O ALA a1039 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N PHE a1041 " --> pdb=" O ILE a1067 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER a1006 " --> pdb=" O VAL a1040 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL a1042 " --> pdb=" O SER a1006 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N HIS a1008 " --> pdb=" O VAL a1042 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE a1007 " --> pdb=" O PHE a1112 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER a1114 " --> pdb=" O ILE a1007 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N VAL a1009 " --> pdb=" O SER a1114 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N PHE a1109 " --> pdb=" O LEU a1141 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N PHE a1143 " --> pdb=" O PHE a1109 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL a1111 " --> pdb=" O PHE a1143 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE a1145 " --> pdb=" O VAL a1111 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N HIS a1113 " --> pdb=" O ILE a1145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 1243 through 1246 removed outlier: 3.682A pdb=" N LEU a1352 " --> pdb=" O CYS a1290 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA a1288 " --> pdb=" O ASN a1354 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY a1295 " --> pdb=" O ASN a1330 " (cutoff:3.500A) 313 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.92 - 1.11: 3681 1.11 - 1.29: 5284 1.29 - 1.48: 3878 1.48 - 1.67: 2336 1.67 - 1.85: 84 Bond restraints: 15263 Sorted by residual: bond pdb=" CA ASN b 50 " pdb=" C ASN b 50 " ideal model delta sigma weight residual 1.523 1.344 0.179 1.34e-02 5.57e+03 1.79e+02 bond pdb=" CA VAL a1298 " pdb=" CB VAL a1298 " ideal model delta sigma weight residual 1.540 1.446 0.094 7.70e-03 1.69e+04 1.48e+02 bond pdb=" N HIS a1257 " pdb=" CA HIS a1257 " ideal model delta sigma weight residual 1.467 1.362 0.105 8.70e-03 1.32e+04 1.46e+02 bond pdb=" CA PRO b 63 " pdb=" C PRO b 63 " ideal model delta sigma weight residual 1.521 1.378 0.143 1.21e-02 6.83e+03 1.40e+02 bond pdb=" CA ASN a1330 " pdb=" C ASN a1330 " ideal model delta sigma weight residual 1.524 1.379 0.145 1.23e-02 6.61e+03 1.39e+02 ... (remaining 15258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.65: 25729 5.65 - 11.29: 1679 11.29 - 16.94: 90 16.94 - 22.59: 8 22.59 - 28.23: 2 Bond angle restraints: 27508 Sorted by residual: angle pdb=" CA HIS b 37 " pdb=" CB HIS b 37 " pdb=" CG HIS b 37 " ideal model delta sigma weight residual 113.80 99.30 14.50 1.00e+00 1.00e+00 2.10e+02 angle pdb=" CA PHE b 343 " pdb=" CB PHE b 343 " pdb=" CG PHE b 343 " ideal model delta sigma weight residual 113.80 99.50 14.30 1.00e+00 1.00e+00 2.05e+02 angle pdb=" CA ASN M3193 " pdb=" CB ASN M3193 " pdb=" CG ASN M3193 " ideal model delta sigma weight residual 112.60 98.67 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA ASN a1200 " pdb=" CB ASN a1200 " pdb=" CG ASN a1200 " ideal model delta sigma weight residual 112.60 98.90 13.70 1.00e+00 1.00e+00 1.88e+02 angle pdb=" CA GLN a1031 " pdb=" C GLN a1031 " pdb=" N PRO a1032 " ideal model delta sigma weight residual 118.44 138.37 -19.93 1.59e+00 3.96e-01 1.57e+02 ... (remaining 27503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.96: 6399 18.96 - 37.91: 499 37.91 - 56.86: 233 56.86 - 75.81: 85 75.81 - 94.77: 25 Dihedral angle restraints: 7241 sinusoidal: 3916 harmonic: 3325 Sorted by residual: dihedral pdb=" CG TRP a1381 " pdb=" CD1 TRP a1381 " pdb=" NE1 TRP a1381 " pdb=" HE1 TRP a1381 " ideal model delta harmonic sigma weight residual 180.00 139.72 40.28 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" N PHE b 214 " pdb=" C PHE b 214 " pdb=" CA PHE b 214 " pdb=" CB PHE b 214 " ideal model delta harmonic sigma weight residual 122.80 104.15 18.65 0 2.50e+00 1.60e-01 5.57e+01 dihedral pdb=" C GLU a1228 " pdb=" N GLU a1228 " pdb=" CA GLU a1228 " pdb=" CB GLU a1228 " ideal model delta harmonic sigma weight residual -122.60 -140.89 18.29 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 7238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.176: 727 0.176 - 0.352: 308 0.352 - 0.529: 87 0.529 - 0.705: 29 0.705 - 0.881: 8 Chirality restraints: 1159 Sorted by residual: chirality pdb=" CA THR b 188 " pdb=" N THR b 188 " pdb=" C THR b 188 " pdb=" CB THR b 188 " both_signs ideal model delta sigma weight residual False 2.53 1.64 0.88 2.00e-01 2.50e+01 1.94e+01 chirality pdb=" CA ARG b 369 " pdb=" N ARG b 369 " pdb=" C ARG b 369 " pdb=" CB ARG b 369 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CA MET a1287 " pdb=" N MET a1287 " pdb=" C MET a1287 " pdb=" CB MET a1287 " both_signs ideal model delta sigma weight residual False 2.51 1.67 0.84 2.00e-01 2.50e+01 1.76e+01 ... (remaining 1156 not shown) Planarity restraints: 2314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 243 " -0.065 9.50e-02 1.11e+02 1.94e-01 8.40e+02 pdb=" NE ARG b 243 " -0.137 2.00e-02 2.50e+03 pdb=" CZ ARG b 243 " -0.176 2.00e-02 2.50e+03 pdb=" NH1 ARG b 243 " -0.080 2.00e-02 2.50e+03 pdb=" NH2 ARG b 243 " -0.176 2.00e-02 2.50e+03 pdb="HH11 ARG b 243 " 0.011 2.00e-02 2.50e+03 pdb="HH12 ARG b 243 " 0.265 2.00e-02 2.50e+03 pdb="HH21 ARG b 243 " -0.111 2.00e-02 2.50e+03 pdb="HH22 ARG b 243 " 0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a1381 " -0.162 2.00e-02 2.50e+03 1.44e-01 8.28e+02 pdb=" CG TRP a1381 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP a1381 " -0.088 2.00e-02 2.50e+03 pdb=" CD2 TRP a1381 " 0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP a1381 " -0.074 2.00e-02 2.50e+03 pdb=" CE2 TRP a1381 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP a1381 " 0.089 2.00e-02 2.50e+03 pdb=" CZ2 TRP a1381 " -0.098 2.00e-02 2.50e+03 pdb=" CZ3 TRP a1381 " 0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP a1381 " -0.051 2.00e-02 2.50e+03 pdb=" HD1 TRP a1381 " -0.034 2.00e-02 2.50e+03 pdb=" HE1 TRP a1381 " 0.461 2.00e-02 2.50e+03 pdb=" HE3 TRP a1381 " 0.117 2.00e-02 2.50e+03 pdb=" HZ2 TRP a1381 " -0.168 2.00e-02 2.50e+03 pdb=" HZ3 TRP a1381 " 0.079 2.00e-02 2.50e+03 pdb=" HH2 TRP a1381 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 224 " -0.402 2.00e-02 2.50e+03 1.63e-01 7.99e+02 pdb=" CG TYR b 224 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR b 224 " 0.129 2.00e-02 2.50e+03 pdb=" CD2 TYR b 224 " 0.141 2.00e-02 2.50e+03 pdb=" CE1 TYR b 224 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 TYR b 224 " 0.083 2.00e-02 2.50e+03 pdb=" CZ TYR b 224 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR b 224 " -0.297 2.00e-02 2.50e+03 pdb=" HD1 TYR b 224 " 0.071 2.00e-02 2.50e+03 pdb=" HD2 TYR b 224 " 0.094 2.00e-02 2.50e+03 pdb=" HE1 TYR b 224 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR b 224 " 0.033 2.00e-02 2.50e+03 ... (remaining 2311 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 1452 2.15 - 2.76: 28697 2.76 - 3.37: 42527 3.37 - 3.99: 58195 3.99 - 4.60: 87032 Nonbonded interactions: 217903 Sorted by model distance: nonbonded pdb=" H LEU a1191 " pdb=" H ASP a1192 " model vdw 1.535 2.100 nonbonded pdb=" HG SER b 126 " pdb=" OE2 GLU b 127 " model vdw 1.535 2.450 nonbonded pdb=" HG1 THR b 287 " pdb=" OE2 GLU b 290 " model vdw 1.543 2.450 nonbonded pdb=" H VAL a1036 " pdb="HG22 VAL a1036 " model vdw 1.549 2.270 nonbonded pdb=" OD2 ASP b 427 " pdb=" HZ1 LYS M3117 " model vdw 1.550 2.450 ... (remaining 217898 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: 0.390 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: 0.240 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.420 Find NCS groups from input model: 0.130 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:2.790 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 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 0.179 7822 Z= 2.565 Angle : 3.433 21.130 10607 Z= 2.287 Chirality : 0.224 0.881 1159 Planarity : 0.036 0.314 1394 Dihedral : 17.770 94.766 2883 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 7.28 % Allowed : 18.61 % Favored : 74.12 % Rotamer: Outliers : 8.39 % Allowed : 11.15 % Favored : 80.46 % Cbeta Deviations : 5.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.45 (0.19), residues: 962 helix: -4.22 (0.14), residues: 449 sheet: -3.68 (0.42), residues: 127 loop : -4.38 (0.25), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.241 0.047 TRP b 407 HIS 0.018 0.004 HIS b 139 PHE 0.255 0.039 PHE b 244 TYR 0.355 0.054 TYR b 224 ARG 0.048 0.007 ARG M3201 Details of bonding type rmsd hydrogen bonds : bond 0.27191 ( 308) hydrogen bonds : angle 11.54697 ( 888) SS BOND : bond 0.06224 ( 1) SS BOND : angle 5.12147 ( 2) covalent geometry : bond 0.03508 ( 7821) covalent geometry : angle 3.43229 (10605) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 90 time to evaluate : 1.154 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 11 GLN cc_start: 0.5255 (OUTLIER) cc_final: 0.4718 (pm20) REVERT: b 117 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8023 (p) REVERT: b 398 MET cc_start: 0.7483 (ptp) cc_final: 0.7162 (mmt) REVERT: a 1005 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6701 (mp) REVERT: a 1075 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.7870 (t0) outliers start: 70 outliers final: 30 residues processed: 154 average time/residue: 0.5143 time to fit residues: 102.2604 Evaluate side-chains 114 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 11 GLN Chi-restraints excluded: chain b residue 39 ASP Chi-restraints excluded: chain b residue 72 PRO Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 117 SER Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 241 CYS Chi-restraints excluded: chain b residue 278 ARG Chi-restraints excluded: chain b residue 292 THR Chi-restraints excluded: chain b residue 294 GLN Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3122 GLU Chi-restraints excluded: chain M residue 3204 LYS Chi-restraints excluded: chain M residue 3206 CYS Chi-restraints excluded: chain a residue 1002 ARG Chi-restraints excluded: chain a residue 1005 ILE Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1106 LEU Chi-restraints excluded: chain a residue 1146 TYR Chi-restraints excluded: chain a residue 1156 VAL Chi-restraints excluded: chain a residue 1217 ARG Chi-restraints excluded: chain a residue 1277 VAL Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1366 ASP Chi-restraints excluded: chain a residue 1376 ARG Chi-restraints excluded: chain a residue 1407 GLU Chi-restraints excluded: chain a residue 1412 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 54 ASN b 101 ASN b 337 ASN b 339 ASN b 433 GLN M3114 ASN M3155 GLN a1018 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.067332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.048974 restraints weight = 119526.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.049834 restraints weight = 64763.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.050510 restraints weight = 45663.658| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7822 Z= 0.231 Angle : 0.886 10.667 10607 Z= 0.482 Chirality : 0.045 0.173 1159 Planarity : 0.008 0.072 1394 Dihedral : 10.794 83.258 1132 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.62 % Allowed : 11.95 % Favored : 87.42 % Rotamer: Outliers : 4.44 % Allowed : 14.87 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.22), residues: 962 helix: -2.96 (0.19), residues: 465 sheet: -2.92 (0.45), residues: 123 loop : -3.48 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a1021 HIS 0.008 0.002 HIS b 6 PHE 0.022 0.002 PHE a1229 TYR 0.028 0.003 TYR a1256 ARG 0.008 0.001 ARG M3181 Details of bonding type rmsd hydrogen bonds : bond 0.06500 ( 308) hydrogen bonds : angle 7.05050 ( 888) SS BOND : bond 0.00869 ( 1) SS BOND : angle 1.34299 ( 2) covalent geometry : bond 0.00490 ( 7821) covalent geometry : angle 0.88552 (10605) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 87 time to evaluate : 1.157 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: b 166 MET cc_start: 0.8655 (mmm) cc_final: 0.8177 (mmm) REVERT: b 259 MET cc_start: 0.9079 (mmm) cc_final: 0.8409 (mmt) REVERT: b 398 MET cc_start: 0.8181 (ptp) cc_final: 0.7464 (mmt) REVERT: M 3183 TYR cc_start: 0.8998 (t80) cc_final: 0.8766 (t80) REVERT: M 3210 TYR cc_start: 0.8635 (t80) cc_final: 0.8378 (t80) REVERT: a 1075 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8239 (t0) REVERT: a 1198 TYR cc_start: 0.2034 (OUTLIER) cc_final: 0.0315 (m-80) outliers start: 37 outliers final: 18 residues processed: 117 average time/residue: 0.5349 time to fit residues: 81.1396 Evaluate side-chains 100 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3125 SER Chi-restraints excluded: chain M residue 3153 ASP Chi-restraints excluded: chain M residue 3204 LYS Chi-restraints excluded: chain M residue 3206 CYS Chi-restraints excluded: chain M residue 3218 ASN Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1376 ARG Chi-restraints excluded: chain a residue 1407 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 32 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 0.2980 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 overall best weight: 6.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 294 GLN b 406 HIS M3166 ASN M3214 ASN a1275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.066671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.051050 restraints weight = 126853.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.052232 restraints weight = 61837.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.053039 restraints weight = 40369.642| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7822 Z= 0.197 Angle : 0.725 7.566 10607 Z= 0.388 Chirality : 0.042 0.145 1159 Planarity : 0.005 0.056 1394 Dihedral : 8.470 81.200 1089 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.67 % Favored : 89.81 % Rotamer: Outliers : 3.72 % Allowed : 15.35 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.24), residues: 962 helix: -2.02 (0.21), residues: 466 sheet: -2.36 (0.47), residues: 122 loop : -2.87 (0.28), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 21 HIS 0.003 0.001 HIS b 107 PHE 0.015 0.002 PHE b 296 TYR 0.014 0.002 TYR a1024 ARG 0.010 0.001 ARG M3181 Details of bonding type rmsd hydrogen bonds : bond 0.04868 ( 308) hydrogen bonds : angle 5.97506 ( 888) SS BOND : bond 0.00503 ( 1) SS BOND : angle 0.59181 ( 2) covalent geometry : bond 0.00405 ( 7821) covalent geometry : angle 0.72483 (10605) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 1.141 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: b 224 TYR cc_start: 0.3068 (OUTLIER) cc_final: 0.0141 (m-80) REVERT: b 235 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8510 (ttp) REVERT: b 259 MET cc_start: 0.9111 (mmm) cc_final: 0.8536 (mmt) REVERT: b 398 MET cc_start: 0.8165 (ptp) cc_final: 0.7495 (mmt) REVERT: M 3122 GLU cc_start: 0.8027 (tt0) cc_final: 0.7609 (tt0) REVERT: M 3183 TYR cc_start: 0.9185 (t80) cc_final: 0.8674 (t80) REVERT: a 1075 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8159 (t0) REVERT: a 1177 MET cc_start: 0.8755 (mmm) cc_final: 0.8326 (mmm) REVERT: a 1198 TYR cc_start: 0.1870 (OUTLIER) cc_final: 0.0154 (m-80) outliers start: 31 outliers final: 18 residues processed: 107 average time/residue: 0.5067 time to fit residues: 71.0947 Evaluate side-chains 100 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 224 TYR Chi-restraints excluded: chain b residue 235 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3114 ASN Chi-restraints excluded: chain M residue 3204 LYS Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1072 ASP Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1412 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 0.2980 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M3214 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.067785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.051668 restraints weight = 121412.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.052751 restraints weight = 62653.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.053534 restraints weight = 40925.799| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7822 Z= 0.142 Angle : 0.636 6.172 10607 Z= 0.332 Chirality : 0.041 0.149 1159 Planarity : 0.005 0.053 1394 Dihedral : 7.525 78.042 1081 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.59 % Favored : 91.89 % Rotamer: Outliers : 2.76 % Allowed : 17.03 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.25), residues: 962 helix: -1.49 (0.22), residues: 474 sheet: -2.18 (0.47), residues: 122 loop : -2.40 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a1021 HIS 0.004 0.001 HIS b 406 PHE 0.017 0.001 PHE M3219 TYR 0.012 0.001 TYR a1024 ARG 0.007 0.000 ARG M3181 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 308) hydrogen bonds : angle 5.34901 ( 888) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.31680 ( 2) covalent geometry : bond 0.00298 ( 7821) covalent geometry : angle 0.63580 (10605) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.130 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: b 224 TYR cc_start: 0.3500 (OUTLIER) cc_final: 0.0439 (m-80) REVERT: b 235 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: b 301 MET cc_start: 0.8722 (mmm) cc_final: 0.8057 (mmm) REVERT: b 398 MET cc_start: 0.8109 (ptp) cc_final: 0.7413 (mmt) REVERT: b 416 MET cc_start: 0.9077 (tpp) cc_final: 0.8709 (tpt) REVERT: M 3183 TYR cc_start: 0.9189 (t80) cc_final: 0.8718 (t80) REVERT: a 1075 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8162 (t0) REVERT: a 1198 TYR cc_start: 0.2095 (OUTLIER) cc_final: 0.0362 (m-80) outliers start: 23 outliers final: 17 residues processed: 98 average time/residue: 0.5334 time to fit residues: 68.7784 Evaluate side-chains 98 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 12 CYS Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 224 TYR Chi-restraints excluded: chain b residue 235 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3131 SER Chi-restraints excluded: chain M residue 3204 LYS Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1216 LEU Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1223 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.066966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.051193 restraints weight = 126922.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.052358 restraints weight = 62300.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.053171 restraints weight = 41082.287| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7822 Z= 0.197 Angle : 0.651 7.584 10607 Z= 0.342 Chirality : 0.041 0.137 1159 Planarity : 0.005 0.053 1394 Dihedral : 7.294 75.959 1081 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.84 % Favored : 90.64 % Rotamer: Outliers : 3.48 % Allowed : 16.79 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.25), residues: 962 helix: -1.17 (0.23), residues: 471 sheet: -2.17 (0.46), residues: 122 loop : -2.31 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a1021 HIS 0.007 0.001 HIS b 406 PHE 0.020 0.002 PHE M3194 TYR 0.015 0.002 TYR a1024 ARG 0.005 0.000 ARG M3181 Details of bonding type rmsd hydrogen bonds : bond 0.04090 ( 308) hydrogen bonds : angle 5.21334 ( 888) SS BOND : bond 0.00503 ( 1) SS BOND : angle 0.93738 ( 2) covalent geometry : bond 0.00411 ( 7821) covalent geometry : angle 0.65065 (10605) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 1.167 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: b 235 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8448 (ttp) REVERT: b 259 MET cc_start: 0.9055 (mmm) cc_final: 0.8276 (mmt) REVERT: b 398 MET cc_start: 0.7878 (ptp) cc_final: 0.7296 (mmt) REVERT: b 416 MET cc_start: 0.9199 (tpp) cc_final: 0.8859 (tpt) REVERT: M 3183 TYR cc_start: 0.9194 (t80) cc_final: 0.8690 (t80) REVERT: a 1075 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8261 (t0) REVERT: a 1177 MET cc_start: 0.8759 (mmm) cc_final: 0.8454 (mmm) REVERT: a 1198 TYR cc_start: 0.1859 (OUTLIER) cc_final: 0.0183 (m-80) outliers start: 29 outliers final: 20 residues processed: 104 average time/residue: 0.5287 time to fit residues: 72.2765 Evaluate side-chains 101 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain b residue 235 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3204 LYS Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1051 GLU Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1072 ASP Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1216 LEU Chi-restraints excluded: chain a residue 1253 GLU Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 40 optimal weight: 9.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 78 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M3211 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.067447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.052028 restraints weight = 125117.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.053225 restraints weight = 59249.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.053835 restraints weight = 38658.845| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7822 Z= 0.175 Angle : 0.617 7.261 10607 Z= 0.320 Chirality : 0.041 0.142 1159 Planarity : 0.004 0.050 1394 Dihedral : 6.975 73.347 1079 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.80 % Favored : 91.79 % Rotamer: Outliers : 3.48 % Allowed : 16.19 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.26), residues: 962 helix: -0.82 (0.23), residues: 470 sheet: -2.10 (0.46), residues: 122 loop : -2.19 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a1021 HIS 0.006 0.001 HIS b 406 PHE 0.012 0.001 PHE b 20 TYR 0.015 0.001 TYR a1024 ARG 0.005 0.000 ARG M3181 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 308) hydrogen bonds : angle 5.02684 ( 888) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.57541 ( 2) covalent geometry : bond 0.00365 ( 7821) covalent geometry : angle 0.61669 (10605) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.103 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: b 235 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8444 (ttp) REVERT: b 259 MET cc_start: 0.9122 (mmm) cc_final: 0.8231 (mmt) REVERT: b 398 MET cc_start: 0.7771 (ptp) cc_final: 0.7236 (mmt) REVERT: M 3152 ARG cc_start: 0.9277 (tpp80) cc_final: 0.8970 (tpm170) REVERT: M 3183 TYR cc_start: 0.9129 (t80) cc_final: 0.8623 (t80) REVERT: a 1075 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8210 (t0) REVERT: a 1198 TYR cc_start: 0.1977 (OUTLIER) cc_final: 0.0089 (m-80) outliers start: 29 outliers final: 23 residues processed: 101 average time/residue: 0.5737 time to fit residues: 75.2848 Evaluate side-chains 101 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain b residue 235 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3204 LYS Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1051 GLU Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1064 GLU Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1072 ASP Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1216 LEU Chi-restraints excluded: chain a residue 1243 LEU Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1351 MET Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1397 GLU Chi-restraints excluded: chain a residue 1412 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 42 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 chunk 82 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 47 optimal weight: 30.0000 chunk 22 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.068049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.052297 restraints weight = 124583.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.053441 restraints weight = 59632.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.054122 restraints weight = 39815.071| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7822 Z= 0.124 Angle : 0.593 6.603 10607 Z= 0.305 Chirality : 0.040 0.147 1159 Planarity : 0.004 0.054 1394 Dihedral : 6.744 69.938 1079 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.90 % Favored : 91.68 % Rotamer: Outliers : 2.76 % Allowed : 17.15 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.27), residues: 962 helix: -0.49 (0.24), residues: 470 sheet: -2.01 (0.46), residues: 125 loop : -1.98 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a1021 HIS 0.005 0.001 HIS a1380 PHE 0.011 0.001 PHE M3194 TYR 0.013 0.001 TYR M3146 ARG 0.004 0.000 ARG M3181 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 308) hydrogen bonds : angle 4.83654 ( 888) SS BOND : bond 0.00367 ( 1) SS BOND : angle 0.70104 ( 2) covalent geometry : bond 0.00268 ( 7821) covalent geometry : angle 0.59324 (10605) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 224 TYR cc_start: 0.3311 (OUTLIER) cc_final: 0.0210 (m-80) REVERT: b 235 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: b 259 MET cc_start: 0.9118 (mmm) cc_final: 0.8484 (mmt) REVERT: b 398 MET cc_start: 0.7780 (ptp) cc_final: 0.7253 (mmt) REVERT: M 3152 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8798 (tpm170) REVERT: M 3183 TYR cc_start: 0.9103 (t80) cc_final: 0.8632 (t80) REVERT: a 1075 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8188 (t0) REVERT: a 1198 TYR cc_start: 0.1803 (OUTLIER) cc_final: 0.0230 (m-80) outliers start: 23 outliers final: 15 residues processed: 98 average time/residue: 0.5409 time to fit residues: 69.0435 Evaluate side-chains 93 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 224 TYR Chi-restraints excluded: chain b residue 235 MET Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1064 GLU Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1072 ASP Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1243 LEU Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 43 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 50.0000 chunk 30 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.067321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.051594 restraints weight = 126036.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.052869 restraints weight = 61268.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053404 restraints weight = 40623.741| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7822 Z= 0.197 Angle : 0.635 7.899 10607 Z= 0.330 Chirality : 0.041 0.140 1159 Planarity : 0.004 0.050 1394 Dihedral : 6.516 67.624 1072 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.32 % Favored : 91.27 % Rotamer: Outliers : 3.24 % Allowed : 17.15 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.26), residues: 962 helix: -0.55 (0.23), residues: 472 sheet: -1.97 (0.47), residues: 123 loop : -2.04 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a1021 HIS 0.007 0.001 HIS b 406 PHE 0.015 0.001 PHE M3219 TYR 0.014 0.002 TYR a1024 ARG 0.004 0.000 ARG M3181 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 308) hydrogen bonds : angle 4.93150 ( 888) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.72452 ( 2) covalent geometry : bond 0.00411 ( 7821) covalent geometry : angle 0.63480 (10605) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 1.143 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: b 259 MET cc_start: 0.9075 (mmm) cc_final: 0.8103 (mmt) REVERT: b 398 MET cc_start: 0.7766 (ptp) cc_final: 0.7270 (mmt) REVERT: M 3152 ARG cc_start: 0.9224 (tpp80) cc_final: 0.8921 (tpm170) REVERT: M 3183 TYR cc_start: 0.9157 (t80) cc_final: 0.8866 (t80) REVERT: a 1075 ASN cc_start: 0.8884 (OUTLIER) cc_final: 0.8258 (t0) REVERT: a 1198 TYR cc_start: 0.2026 (OUTLIER) cc_final: 0.0156 (m-80) outliers start: 27 outliers final: 22 residues processed: 94 average time/residue: 0.4877 time to fit residues: 60.9154 Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 191 VAL Chi-restraints excluded: chain b residue 195 VAL Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3109 GLN Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1051 GLU Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1072 ASP Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1243 LEU Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Chi-restraints excluded: chain a residue 1397 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.067776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.052353 restraints weight = 124772.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053482 restraints weight = 61016.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.054265 restraints weight = 41060.796| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7822 Z= 0.140 Angle : 0.612 7.305 10607 Z= 0.314 Chirality : 0.041 0.143 1159 Planarity : 0.004 0.048 1394 Dihedral : 6.331 63.507 1072 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.80 % Favored : 91.79 % Rotamer: Outliers : 2.52 % Allowed : 17.15 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.27), residues: 962 helix: -0.38 (0.23), residues: 471 sheet: -1.98 (0.47), residues: 122 loop : -1.88 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 21 HIS 0.005 0.001 HIS a1380 PHE 0.015 0.001 PHE b 20 TYR 0.012 0.001 TYR M3146 ARG 0.012 0.000 ARG M3159 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 308) hydrogen bonds : angle 4.80520 ( 888) SS BOND : bond 0.00413 ( 1) SS BOND : angle 0.64295 ( 2) covalent geometry : bond 0.00299 ( 7821) covalent geometry : angle 0.61151 (10605) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 1.147 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: b 224 TYR cc_start: 0.3621 (OUTLIER) cc_final: 0.0442 (m-80) REVERT: b 235 MET cc_start: 0.8862 (ttp) cc_final: 0.8317 (ttp) REVERT: b 259 MET cc_start: 0.9151 (mmm) cc_final: 0.8485 (mmt) REVERT: b 398 MET cc_start: 0.7873 (ptp) cc_final: 0.7383 (mmt) REVERT: M 3152 ARG cc_start: 0.9257 (tpp80) cc_final: 0.8936 (tpm170) REVERT: M 3183 TYR cc_start: 0.9247 (t80) cc_final: 0.9013 (t80) REVERT: a 1075 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8226 (t0) REVERT: a 1198 TYR cc_start: 0.1922 (OUTLIER) cc_final: 0.0206 (m-80) outliers start: 21 outliers final: 16 residues processed: 93 average time/residue: 0.4733 time to fit residues: 59.0904 Evaluate side-chains 91 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 115 VAL Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 224 TYR Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3109 GLN Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1072 ASP Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1243 LEU Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 49 optimal weight: 50.0000 chunk 78 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 93 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.067579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.052270 restraints weight = 126307.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.053386 restraints weight = 62219.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.054012 restraints weight = 40684.472| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7822 Z= 0.182 Angle : 0.638 8.135 10607 Z= 0.331 Chirality : 0.041 0.141 1159 Planarity : 0.005 0.048 1394 Dihedral : 6.328 59.192 1072 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.94 % Favored : 90.64 % Rotamer: Outliers : 2.28 % Allowed : 17.63 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.27), residues: 962 helix: -0.37 (0.23), residues: 471 sheet: -2.02 (0.47), residues: 123 loop : -1.89 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP M3212 HIS 0.006 0.001 HIS b 406 PHE 0.013 0.001 PHE b 20 TYR 0.013 0.001 TYR a1024 ARG 0.009 0.001 ARG M3159 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 308) hydrogen bonds : angle 4.88740 ( 888) SS BOND : bond 0.00360 ( 1) SS BOND : angle 0.76362 ( 2) covalent geometry : bond 0.00382 ( 7821) covalent geometry : angle 0.63787 (10605) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 1.113 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: b 235 MET cc_start: 0.8905 (ttp) cc_final: 0.8248 (ttp) REVERT: b 398 MET cc_start: 0.7862 (ptp) cc_final: 0.7420 (mmt) REVERT: M 3152 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8922 (tpm170) REVERT: M 3183 TYR cc_start: 0.9246 (t80) cc_final: 0.9016 (t80) REVERT: a 1075 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8211 (t0) REVERT: a 1198 TYR cc_start: 0.2054 (OUTLIER) cc_final: 0.0291 (m-80) outliers start: 19 outliers final: 16 residues processed: 91 average time/residue: 0.4702 time to fit residues: 57.7354 Evaluate side-chains 92 residues out of total 834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 94 PHE Chi-restraints excluded: chain b residue 122 VAL Chi-restraints excluded: chain b residue 200 GLU Chi-restraints excluded: chain b residue 326 LYS Chi-restraints excluded: chain b residue 427 ASP Chi-restraints excluded: chain M residue 3109 GLN Chi-restraints excluded: chain a residue 1006 SER Chi-restraints excluded: chain a residue 1011 GLN Chi-restraints excluded: chain a residue 1025 CYS Chi-restraints excluded: chain a residue 1062 HIS Chi-restraints excluded: chain a residue 1065 GLN Chi-restraints excluded: chain a residue 1072 ASP Chi-restraints excluded: chain a residue 1075 ASN Chi-restraints excluded: chain a residue 1121 SER Chi-restraints excluded: chain a residue 1198 TYR Chi-restraints excluded: chain a residue 1331 TYR Chi-restraints excluded: chain a residue 1352 LEU Chi-restraints excluded: chain a residue 1355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 50.0000 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.067661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.051861 restraints weight = 125000.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.052959 restraints weight = 64118.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.053678 restraints weight = 43923.841| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7822 Z= 0.200 Angle : 0.648 8.922 10607 Z= 0.336 Chirality : 0.041 0.139 1159 Planarity : 0.005 0.050 1394 Dihedral : 6.271 51.388 1071 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.63 % Favored : 90.96 % Rotamer: Outliers : 2.16 % Allowed : 17.87 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.27), residues: 962 helix: -0.36 (0.24), residues: 471 sheet: -2.05 (0.47), residues: 123 loop : -1.89 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP M3212 HIS 0.006 0.001 HIS a1380 PHE 0.013 0.001 PHE b 20 TYR 0.014 0.002 TYR a1024 ARG 0.008 0.001 ARG M3159 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 308) hydrogen bonds : angle 4.93235 ( 888) SS BOND : bond 0.00403 ( 1) SS BOND : angle 0.86901 ( 2) covalent geometry : bond 0.00417 ( 7821) covalent geometry : angle 0.64749 (10605) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4470.51 seconds wall clock time: 77 minutes 18.96 seconds (4638.96 seconds total)