Starting phenix.real_space_refine on Sun Dec 10 16:51:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiq_9997/12_2023/6kiq_9997.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiq_9997/12_2023/6kiq_9997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiq_9997/12_2023/6kiq_9997.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiq_9997/12_2023/6kiq_9997.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiq_9997/12_2023/6kiq_9997.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kiq_9997/12_2023/6kiq_9997.pdb" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 54 5.16 5 C 4827 2.51 5 N 1310 2.21 5 O 1458 1.98 5 H 7444 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a GLU 1027": "OE1" <-> "OE2" Residue "a ASP 1043": "OD1" <-> "OD2" Residue "a GLU 1045": "OE1" <-> "OE2" Residue "a TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1064": "OE1" <-> "OE2" Residue "a TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 1082": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 1090": "OD1" <-> "OD2" Residue "a ASP 1094": "OD1" <-> "OD2" Residue "a PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1129": "OE1" <-> "OE2" Residue "a GLU 1142": "OE1" <-> "OE2" Residue "a TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1157": "OE1" <-> "OE2" Residue "a TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1170": "OE1" <-> "OE2" Residue "a TYR 1184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 1192": "OD1" <-> "OD2" Residue "a ASP 1219": "OD1" <-> "OD2" Residue "a ASP 1225": "OD1" <-> "OD2" Residue "a PHE 1229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 1246": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1258": "OE1" <-> "OE2" Residue "a GLU 1271": "OE1" <-> "OE2" Residue "a TYR 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 1373": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 1382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1403": "OE1" <-> "OE2" Residue "a ASP 1405": "OD1" <-> "OD2" Residue "a TYR 1406": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b ASP 31": "OD1" <-> "OD2" Residue "b TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 47": "OE1" <-> "OE2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 71": "OE1" <-> "OE2" Residue "b PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 110": "OE1" <-> "OE2" Residue "b ASP 120": "OD1" <-> "OD2" Residue "b ASP 130": "OD1" <-> "OD2" Residue "b PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 159": "OE1" <-> "OE2" Residue "b TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 205": "OD1" <-> "OD2" Residue "b GLU 207": "OE1" <-> "OE2" Residue "b TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 226": "OD1" <-> "OD2" Residue "b PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 345": "OE1" <-> "OE2" Residue "b PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 411": "OE1" <-> "OE2" Residue "b ASP 414": "OD1" <-> "OD2" Residue "b GLU 420": "OE1" <-> "OE2" Residue "b TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 3102": "OE1" <-> "OE2" Residue "M GLU 3107": "OE1" <-> "OE2" Residue "M GLU 3138": "OE1" <-> "OE2" Residue "M TYR 3146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 3170": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 3171": "OD1" <-> "OD2" Residue "M GLU 3185": "OE1" <-> "OE2" Residue "M GLU 3186": "OE1" <-> "OE2" Residue "M PHE 3188": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 3196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 3197": "OE1" <-> "OE2" Residue "M GLU 3224": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15093 Number of models: 1 Model: "" Number of chains: 3 Chain: "a" Number of atoms: 6375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6375 Classifications: {'peptide': 412} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 392} Chain: "b" Number of atoms: 6584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6584 Classifications: {'peptide': 426} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 405} Chain: "M" Number of atoms: 2134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2134 Classifications: {'peptide': 130} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 123} Time building chain proxies: 7.19, per 1000 atoms: 0.48 Number of scatterers: 15093 At special positions: 0 Unit cell: (79.2, 106.92, 112.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 54 16.00 O 1458 8.00 N 1310 7.00 C 4827 6.00 H 7444 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.36 Conformation dependent library (CDL) restraints added in 1.7 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 54.4% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'a' and resid 1010 through 1029 removed outlier: 3.535A pdb=" N GLN a1015 " --> pdb=" O GLN a1011 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU a1022 " --> pdb=" O ASN a1018 " (cutoff:3.500A) Processing helix chain 'a' and resid 1046 through 1055 removed outlier: 3.800A pdb=" N VAL a1052 " --> pdb=" O VAL a1048 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR a1054 " --> pdb=" O ASP a1050 " (cutoff:3.500A) Processing helix chain 'a' and resid 1062 through 1064 No H-bonds generated for 'chain 'a' and resid 1062 through 1064' Processing helix chain 'a' and resid 1076 through 1082 removed outlier: 3.918A pdb=" N GLY a1080 " --> pdb=" O ASN a1076 " (cutoff:3.500A) Processing helix chain 'a' and resid 1082 through 1101 removed outlier: 4.515A pdb=" N GLU a1087 " --> pdb=" O THR a1083 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE a1088 " --> pdb=" O ILE a1084 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASP a1090 " --> pdb=" O LYS a1086 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N LEU a1091 " --> pdb=" O GLU a1087 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG a1095 " --> pdb=" O LEU a1091 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE a1096 " --> pdb=" O VAL a1092 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG a1097 " --> pdb=" O LEU a1093 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP a1101 " --> pdb=" O ARG a1097 " (cutoff:3.500A) Processing helix chain 'a' and resid 1121 through 1135 removed outlier: 3.727A pdb=" N GLU a1129 " --> pdb=" O SER a1125 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL a1133 " --> pdb=" O GLU a1129 " (cutoff:3.500A) Processing helix chain 'a' and resid 1156 through 1170 removed outlier: 3.561A pdb=" N THR a1165 " --> pdb=" O SER a1161 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N HIS a1166 " --> pdb=" O ILE a1162 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR a1167 " --> pdb=" O LEU a1163 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU a1170 " --> pdb=" O HIS a1166 " (cutoff:3.500A) Processing helix chain 'a' and resid 1179 through 1190 removed outlier: 3.994A pdb=" N ASP a1185 " --> pdb=" O GLU a1181 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE a1186 " --> pdb=" O ALA a1182 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS a1187 " --> pdb=" O ILE a1183 " (cutoff:3.500A) Processing helix chain 'a' and resid 1197 through 1217 removed outlier: 3.600A pdb=" N LEU a1201 " --> pdb=" O THR a1197 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG a1203 " --> pdb=" O THR a1199 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN a1207 " --> pdb=" O ARG a1203 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER a1210 " --> pdb=" O GLY a1206 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE a1212 " --> pdb=" O ILE a1208 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR a1213 " --> pdb=" O VAL a1209 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA a1214 " --> pdb=" O SER a1210 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N SER a1215 " --> pdb=" O SER a1211 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU a1216 " --> pdb=" O ILE a1212 " (cutoff:3.500A) Processing helix chain 'a' and resid 1225 through 1233 removed outlier: 3.681A pdb=" N PHE a1229 " --> pdb=" O ASP a1225 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN a1230 " --> pdb=" O LEU a1226 " (cutoff:3.500A) Processing helix chain 'a' and resid 1261 through 1271 removed outlier: 3.655A pdb=" N ASN a1267 " --> pdb=" O ALA a1263 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS a1269 " --> pdb=" O ILE a1265 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE a1270 " --> pdb=" O THR a1266 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU a1271 " --> pdb=" O ASN a1267 " (cutoff:3.500A) Processing helix chain 'a' and resid 1280 through 1284 removed outlier: 4.332A pdb=" N HIS a1283 " --> pdb=" O ASP a1280 " (cutoff:3.500A) Processing helix chain 'a' and resid 1298 through 1311 removed outlier: 3.711A pdb=" N VAL a1302 " --> pdb=" O VAL a1298 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA a1307 " --> pdb=" O ASN a1303 " (cutoff:3.500A) Processing helix chain 'a' and resid 1358 through 1376 removed outlier: 3.508A pdb=" N ARG a1364 " --> pdb=" O GLU a1360 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU a1365 " --> pdb=" O ALA a1361 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU a1371 " --> pdb=" O HIS a1367 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET a1372 " --> pdb=" O LYS a1368 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS a1375 " --> pdb=" O LEU a1371 " (cutoff:3.500A) Processing helix chain 'a' and resid 1379 through 1384 removed outlier: 3.554A pdb=" N GLY a1384 " --> pdb=" O HIS a1380 " (cutoff:3.500A) Processing helix chain 'a' and resid 1388 through 1404 removed outlier: 3.628A pdb=" N PHE a1392 " --> pdb=" O GLU a1388 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET a1399 " --> pdb=" O ALA a1395 " (cutoff:3.500A) Processing helix chain 'a' and resid 1404 through 1409 Processing helix chain 'b' and resid 10 through 27 removed outlier: 4.299A pdb=" N GLY b 17 " --> pdb=" O GLY b 13 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS b 19 " --> pdb=" O GLN b 15 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU b 22 " --> pdb=" O ALA b 18 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP b 26 " --> pdb=" O GLU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 47 removed outlier: 4.145A pdb=" N LEU b 44 " --> pdb=" O SER b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 48 through 52 Processing helix chain 'b' and resid 74 through 79 Processing helix chain 'b' and resid 88 through 90 No H-bonds generated for 'chain 'b' and resid 88 through 90' Processing helix chain 'b' and resid 103 through 107 Processing helix chain 'b' and resid 110 through 115 Processing helix chain 'b' and resid 115 through 127 removed outlier: 4.246A pdb=" N VAL b 121 " --> pdb=" O SER b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 143 through 148 removed outlier: 4.224A pdb=" N SER b 147 " --> pdb=" O GLY b 143 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY b 148 " --> pdb=" O GLY b 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 143 through 148' Processing helix chain 'b' and resid 148 through 161 removed outlier: 4.334A pdb=" N SER b 155 " --> pdb=" O THR b 151 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS b 156 " --> pdb=" O LEU b 152 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU b 159 " --> pdb=" O SER b 155 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 195 removed outlier: 3.589A pdb=" N ASN b 186 " --> pdb=" O VAL b 182 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER b 190 " --> pdb=" O ASN b 186 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS b 192 " --> pdb=" O THR b 188 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN b 193 " --> pdb=" O LEU b 189 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 215 removed outlier: 3.779A pdb=" N CYS b 213 " --> pdb=" O LEU b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 223 through 238 removed outlier: 3.520A pdb=" N LEU b 227 " --> pdb=" O THR b 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA b 233 " --> pdb=" O HIS b 229 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR b 234 " --> pdb=" O LEU b 230 " (cutoff:3.500A) Processing helix chain 'b' and resid 239 through 244 Processing helix chain 'b' and resid 251 through 258 removed outlier: 3.679A pdb=" N ALA b 256 " --> pdb=" O LEU b 252 " (cutoff:3.500A) Processing helix chain 'b' and resid 277 through 281 removed outlier: 3.636A pdb=" N GLN b 281 " --> pdb=" O ARG b 278 " (cutoff:3.500A) Processing helix chain 'b' and resid 288 through 296 Processing helix chain 'b' and resid 306 through 310 removed outlier: 3.545A pdb=" N HIS b 309 " --> pdb=" O ASP b 306 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 339 removed outlier: 3.596A pdb=" N VAL b 328 " --> pdb=" O SER b 324 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP b 329 " --> pdb=" O MET b 325 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU b 333 " --> pdb=" O ASP b 329 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN b 339 " --> pdb=" O VAL b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 340 through 343 removed outlier: 3.836A pdb=" N PHE b 343 " --> pdb=" O SER b 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 340 through 343' Processing helix chain 'b' and resid 381 through 383 No H-bonds generated for 'chain 'b' and resid 381 through 383' Processing helix chain 'b' and resid 384 through 400 removed outlier: 4.290A pdb=" N PHE b 388 " --> pdb=" O ILE b 384 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ARG b 390 " --> pdb=" O GLU b 386 " (cutoff:3.500A) Processing helix chain 'b' and resid 405 through 410 Processing helix chain 'b' and resid 415 through 435 removed outlier: 3.662A pdb=" N VAL b 429 " --> pdb=" O MET b 425 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR b 435 " --> pdb=" O GLU b 431 " (cutoff:3.500A) Processing helix chain 'M' and resid 3103 through 3114 removed outlier: 3.589A pdb=" N GLN M3109 " --> pdb=" O ILE M3105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG M3110 " --> pdb=" O LEU M3106 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS M3113 " --> pdb=" O GLN M3109 " (cutoff:3.500A) Processing helix chain 'M' and resid 3116 through 3126 removed outlier: 3.697A pdb=" N LEU M3120 " --> pdb=" O LYS M3116 " (cutoff:3.500A) Processing helix chain 'M' and resid 3130 through 3145 removed outlier: 3.813A pdb=" N VAL M3136 " --> pdb=" O GLY M3132 " (cutoff:3.500A) Processing helix chain 'M' and resid 3150 through 3159 Processing helix chain 'M' and resid 3161 through 3170 removed outlier: 4.393A pdb=" N HIS M3165 " --> pdb=" O ASP M3161 " (cutoff:3.500A) Processing helix chain 'M' and resid 3179 through 3189 Processing helix chain 'M' and resid 3195 through 3203 removed outlier: 3.515A pdb=" N ILE M3199 " --> pdb=" O THR M3195 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER M3203 " --> pdb=" O ILE M3199 " (cutoff:3.500A) Processing helix chain 'M' and resid 3205 through 3219 Processing sheet with id=AA1, first strand: chain 'a' and resid 1066 through 1068 removed outlier: 5.653A pdb=" N PHE a1041 " --> pdb=" O ILE a1067 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER a1006 " --> pdb=" O VAL a1040 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL a1042 " --> pdb=" O SER a1006 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N HIS a1008 " --> pdb=" O VAL a1042 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 1242 through 1243 removed outlier: 5.795A pdb=" N ASN a1354 " --> pdb=" O MET a1287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 1328 through 1330 removed outlier: 3.893A pdb=" N LEU a1292 " --> pdb=" O CYS a1350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 92 through 94 removed outlier: 6.436A pdb=" N LEU b 67 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL b 68 " --> pdb=" O HIS b 6 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLN b 8 " --> pdb=" O VAL b 68 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLU b 3 " --> pdb=" O GLN b 133 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE b 135 " --> pdb=" O GLU b 3 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL b 5 " --> pdb=" O PHE b 135 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N LEU b 137 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE b 7 " --> pdb=" O LEU b 137 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N HIS b 139 " --> pdb=" O ILE b 7 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ALA b 9 " --> pdb=" O HIS b 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE b 165 " --> pdb=" O GLN b 133 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N MET b 166 " --> pdb=" O GLU b 200 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N TYR b 202 " --> pdb=" O MET b 166 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR b 168 " --> pdb=" O TYR b 202 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N THR b 201 " --> pdb=" O PHE b 268 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR b 376 " --> pdb=" O VAL b 318 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA b 354 " --> pdb=" O PHE b 319 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 55 through 56 285 hydrogen bonds defined for protein. 813 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 7420 1.13 - 1.31: 1858 1.31 - 1.49: 3744 1.49 - 1.67: 2159 1.67 - 1.84: 84 Bond restraints: 15265 Sorted by residual: bond pdb=" CA PRO b 63 " pdb=" C PRO b 63 " ideal model delta sigma weight residual 1.521 1.375 0.146 1.21e-02 6.83e+03 1.46e+02 bond pdb=" CA TYR a1024 " pdb=" C TYR a1024 " ideal model delta sigma weight residual 1.523 1.364 0.159 1.34e-02 5.57e+03 1.41e+02 bond pdb=" C MET b 269 " pdb=" N PRO b 270 " ideal model delta sigma weight residual 1.331 1.179 0.152 1.31e-02 5.83e+03 1.34e+02 bond pdb=" CA CYS a1350 " pdb=" C CYS a1350 " ideal model delta sigma weight residual 1.526 1.390 0.135 1.22e-02 6.72e+03 1.23e+02 bond pdb=" CA VAL b 288 " pdb=" C VAL b 288 " ideal model delta sigma weight residual 1.524 1.409 0.115 1.05e-02 9.07e+03 1.21e+02 ... (remaining 15260 not shown) Histogram of bond angle deviations from ideal: 89.60 - 99.54: 105 99.54 - 109.48: 9816 109.48 - 119.42: 11873 119.42 - 129.35: 5633 129.35 - 139.29: 83 Bond angle restraints: 27510 Sorted by residual: angle pdb=" N THR a1231 " pdb=" CA THR a1231 " pdb=" C THR a1231 " ideal model delta sigma weight residual 111.03 126.98 -15.95 1.11e+00 8.12e-01 2.06e+02 angle pdb=" N VAL b 318 " pdb=" CA VAL b 318 " pdb=" CB VAL b 318 " ideal model delta sigma weight residual 112.28 97.93 14.35 1.00e+00 1.00e+00 2.06e+02 angle pdb=" CA HIS b 37 " pdb=" CB HIS b 37 " pdb=" CG HIS b 37 " ideal model delta sigma weight residual 113.80 99.70 14.10 1.00e+00 1.00e+00 1.99e+02 angle pdb=" CA ALA b 273 " pdb=" C ALA b 273 " pdb=" N PRO b 274 " ideal model delta sigma weight residual 118.44 139.29 -20.85 1.59e+00 3.96e-01 1.72e+02 angle pdb=" CA PHE a1176 " pdb=" CB PHE a1176 " pdb=" CG PHE a1176 " ideal model delta sigma weight residual 113.80 101.01 12.79 1.00e+00 1.00e+00 1.64e+02 ... (remaining 27505 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 6030 17.92 - 35.84: 675 35.84 - 53.75: 205 53.75 - 71.67: 103 71.67 - 89.59: 26 Dihedral angle restraints: 7039 sinusoidal: 3714 harmonic: 3325 Sorted by residual: dihedral pdb=" CA THR a1119 " pdb=" C THR a1119 " pdb=" N GLY a1120 " pdb=" CA GLY a1120 " ideal model delta harmonic sigma weight residual -180.00 -98.21 -81.79 0 5.00e+00 4.00e-02 2.68e+02 dihedral pdb=" N THR b 240 " pdb=" C THR b 240 " pdb=" CA THR b 240 " pdb=" CB THR b 240 " ideal model delta harmonic sigma weight residual 123.40 150.45 -27.05 0 2.50e+00 1.60e-01 1.17e+02 dihedral pdb=" N MET b 235 " pdb=" C MET b 235 " pdb=" CA MET b 235 " pdb=" CB MET b 235 " ideal model delta harmonic sigma weight residual 122.80 148.22 -25.42 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 7036 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 819 0.243 - 0.486: 239 0.486 - 0.729: 84 0.729 - 0.972: 14 0.972 - 1.215: 3 Chirality restraints: 1159 Sorted by residual: chirality pdb=" CA MET b 235 " pdb=" N MET b 235 " pdb=" C MET b 235 " pdb=" CB MET b 235 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" CA THR b 240 " pdb=" N THR b 240 " pdb=" C THR b 240 " pdb=" CB THR b 240 " both_signs ideal model delta sigma weight residual False 2.53 1.35 1.18 2.00e-01 2.50e+01 3.47e+01 chirality pdb=" CA TYR a1159 " pdb=" N TYR a1159 " pdb=" C TYR a1159 " pdb=" CB TYR a1159 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 1156 not shown) Planarity restraints: 2314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a1024 " -0.478 2.00e-02 2.50e+03 2.01e-01 1.21e+03 pdb=" CG TYR a1024 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR a1024 " 0.166 2.00e-02 2.50e+03 pdb=" CD2 TYR a1024 " 0.159 2.00e-02 2.50e+03 pdb=" CE1 TYR a1024 " 0.112 2.00e-02 2.50e+03 pdb=" CE2 TYR a1024 " 0.123 2.00e-02 2.50e+03 pdb=" CZ TYR a1024 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR a1024 " -0.386 2.00e-02 2.50e+03 pdb=" HD1 TYR a1024 " 0.113 2.00e-02 2.50e+03 pdb=" HD2 TYR a1024 " 0.099 2.00e-02 2.50e+03 pdb=" HE1 TYR a1024 " 0.037 2.00e-02 2.50e+03 pdb=" HE2 TYR a1024 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG b 253 " -0.318 9.50e-02 1.11e+02 2.48e-01 1.14e+03 pdb=" NE ARG b 253 " -0.198 2.00e-02 2.50e+03 pdb=" CZ ARG b 253 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG b 253 " 0.150 2.00e-02 2.50e+03 pdb=" NH2 ARG b 253 " -0.040 2.00e-02 2.50e+03 pdb="HH11 ARG b 253 " -0.479 2.00e-02 2.50e+03 pdb="HH12 ARG b 253 " 0.359 2.00e-02 2.50e+03 pdb="HH21 ARG b 253 " 0.160 2.00e-02 2.50e+03 pdb="HH22 ARG b 253 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a1362 " 0.521 2.00e-02 2.50e+03 1.66e-01 1.10e+03 pdb=" CG TRP a1362 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP a1362 " -0.126 2.00e-02 2.50e+03 pdb=" CD2 TRP a1362 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP a1362 " -0.103 2.00e-02 2.50e+03 pdb=" CE2 TRP a1362 " -0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP a1362 " -0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP a1362 " 0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP a1362 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP a1362 " 0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP a1362 " -0.192 2.00e-02 2.50e+03 pdb=" HE1 TRP a1362 " 0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP a1362 " -0.213 2.00e-02 2.50e+03 pdb=" HZ2 TRP a1362 " 0.105 2.00e-02 2.50e+03 pdb=" HZ3 TRP a1362 " -0.080 2.00e-02 2.50e+03 pdb=" HH2 TRP a1362 " 0.144 2.00e-02 2.50e+03 ... (remaining 2311 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 869 2.05 - 2.69: 23947 2.69 - 3.33: 43622 3.33 - 3.96: 58367 3.96 - 4.60: 88648 Nonbonded interactions: 215453 Sorted by model distance: nonbonded pdb=" H HIS M3175 " pdb=" H MET M3176 " model vdw 1.418 2.100 nonbonded pdb=" HG1 THR b 239 " pdb="HD21 LEU b 252 " model vdw 1.455 2.270 nonbonded pdb=" H ILE a1315 " pdb="HG22 ILE a1315 " model vdw 1.477 2.270 nonbonded pdb="HH22 ARG b 243 " pdb=" OD2 ASP b 251 " model vdw 1.496 1.850 nonbonded pdb=" OE2 GLU b 200 " pdb=" HH TYR b 202 " model vdw 1.496 1.850 ... (remaining 215448 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.290 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: 0.230 Extract box with map and model: 2.100 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 52.900 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.035 0.159 7821 Z= 2.267 Angle : 3.740 20.852 10605 Z= 2.483 Chirality : 0.266 1.215 1159 Planarity : 0.041 0.330 1394 Dihedral : 19.808 89.588 2883 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 10.71 % Allowed : 18.61 % Favored : 70.69 % Rotamer: Outliers : 14.75 % Allowed : 14.27 % Favored : 70.98 % Cbeta Deviations : 16.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.44 % Twisted General : 2.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.77 (0.18), residues: 962 helix: -4.26 (0.14), residues: 444 sheet: -3.68 (0.42), residues: 121 loop : -4.93 (0.22), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.316 0.057 TRP a1362 HIS 0.018 0.005 HIS a1257 PHE 0.205 0.043 PHE a1112 TYR 0.421 0.063 TYR a1024 ARG 0.049 0.005 ARG a1079 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 126 time to evaluate : 1.236 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 outliers start: 123 outliers final: 66 residues processed: 234 average time/residue: 0.5120 time to fit residues: 155.3357 Evaluate side-chains 170 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 104 time to evaluate : 1.289 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 10 residues processed: 66 average time/residue: 0.2369 time to fit residues: 26.6396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1008 HIS a1102 GLN a1166 HIS a1180 ASN a1274 ASN b 300 ASN b 331 GLN b 337 ASN M3216 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 7821 Z= 0.407 Angle : 1.036 11.138 10605 Z= 0.554 Chirality : 0.049 0.171 1159 Planarity : 0.011 0.137 1394 Dihedral : 9.375 83.119 1056 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 1.35 % Allowed : 15.59 % Favored : 83.06 % Rotamer: Outliers : 4.44 % Allowed : 20.62 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.87 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.20), residues: 962 helix: -3.25 (0.18), residues: 450 sheet: -3.33 (0.44), residues: 120 loop : -4.30 (0.24), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP b 407 HIS 0.014 0.002 HIS b 28 PHE 0.020 0.003 PHE b 169 TYR 0.019 0.002 TYR b 435 ARG 0.008 0.001 ARG a1396 *********************** 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 146 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 109 time to evaluate : 1.259 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 outliers start: 37 outliers final: 18 residues processed: 141 average time/residue: 0.5357 time to fit residues: 98.0752 Evaluate side-chains 117 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.213 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 18 average time/residue: 0.3434 time to fit residues: 10.2707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 94 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN b 28 HIS b 50 ASN b 336 GLN M3109 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.5278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7821 Z= 0.249 Angle : 0.783 9.037 10605 Z= 0.413 Chirality : 0.043 0.159 1159 Planarity : 0.007 0.070 1394 Dihedral : 7.945 81.794 1056 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.94 % Allowed : 13.10 % Favored : 85.97 % Rotamer: Outliers : 2.76 % Allowed : 20.14 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (0.22), residues: 962 helix: -2.29 (0.20), residues: 445 sheet: -3.08 (0.46), residues: 115 loop : -3.93 (0.25), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M3151 HIS 0.007 0.001 HIS b 6 PHE 0.014 0.002 PHE b 83 TYR 0.016 0.002 TYR a1146 ARG 0.006 0.001 ARG a1396 *********************** 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 133 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.426 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 outliers start: 23 outliers final: 9 residues processed: 127 average time/residue: 0.5537 time to fit residues: 91.7194 Evaluate side-chains 109 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 1.366 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.1884 time to fit residues: 4.6453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 58 optimal weight: 0.4980 chunk 87 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1274 ASN b 294 GLN b 406 HIS M3166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.5950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7821 Z= 0.184 Angle : 0.679 7.154 10605 Z= 0.351 Chirality : 0.041 0.139 1159 Planarity : 0.006 0.077 1394 Dihedral : 6.838 80.222 1056 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.83 % Allowed : 10.60 % Favored : 88.57 % Rotamer: Outliers : 1.56 % Allowed : 20.14 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.24), residues: 962 helix: -1.45 (0.22), residues: 461 sheet: -2.85 (0.43), residues: 130 loop : -3.66 (0.27), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M3151 HIS 0.004 0.001 HIS a1380 PHE 0.009 0.001 PHE b 377 TYR 0.015 0.001 TYR b 312 ARG 0.003 0.000 ARG a1396 *********************** 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 123 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 110 time to evaluate : 1.200 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 outliers start: 13 outliers final: 3 residues processed: 119 average time/residue: 0.5549 time to fit residues: 85.1561 Evaluate side-chains 104 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.203 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.2193 time to fit residues: 2.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.0770 chunk 83 optimal weight: 50.0000 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1075 ASN a1274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7821 Z= 0.197 Angle : 0.645 6.982 10605 Z= 0.331 Chirality : 0.041 0.135 1159 Planarity : 0.005 0.075 1394 Dihedral : 6.450 81.516 1056 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.62 % Allowed : 10.40 % Favored : 88.98 % Rotamer: Outliers : 1.80 % Allowed : 20.02 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.25), residues: 962 helix: -1.06 (0.23), residues: 460 sheet: -2.77 (0.44), residues: 130 loop : -3.51 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M3151 HIS 0.004 0.001 HIS b 406 PHE 0.011 0.001 PHE b 377 TYR 0.025 0.002 TYR M3170 ARG 0.003 0.000 ARG a1396 *********************** 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 117 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 1.269 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 outliers start: 15 outliers final: 8 residues processed: 112 average time/residue: 0.5570 time to fit residues: 81.2468 Evaluate side-chains 106 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.296 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.1976 time to fit residues: 4.4523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 50.0000 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 92 optimal weight: 30.0000 chunk 77 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1075 ASN ** b 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 293 GLN b 334 ASN M3166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.6291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7821 Z= 0.360 Angle : 0.718 7.409 10605 Z= 0.375 Chirality : 0.043 0.161 1159 Planarity : 0.006 0.072 1394 Dihedral : 6.778 89.757 1056 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.68 % Favored : 86.69 % Rotamer: Outliers : 2.16 % Allowed : 20.02 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.25), residues: 962 helix: -1.08 (0.23), residues: 451 sheet: -2.95 (0.42), residues: 132 loop : -3.44 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a1021 HIS 0.008 0.001 HIS b 406 PHE 0.016 0.002 PHE b 377 TYR 0.022 0.002 TYR M3146 ARG 0.004 0.001 ARG M3152 *********************** 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 118 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 100 time to evaluate : 1.184 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 outliers start: 18 outliers final: 6 residues processed: 115 average time/residue: 0.5589 time to fit residues: 84.4351 Evaluate side-chains 99 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 1.367 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.2114 time to fit residues: 3.9928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1075 ASN a1346 GLN ** b 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7821 Z= 0.250 Angle : 0.663 6.437 10605 Z= 0.343 Chirality : 0.041 0.139 1159 Planarity : 0.005 0.072 1394 Dihedral : 6.486 85.934 1056 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.06 % Favored : 87.32 % Rotamer: Outliers : 0.72 % Allowed : 22.18 % Favored : 77.10 % 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: -3.21 (0.25), residues: 962 helix: -0.91 (0.23), residues: 459 sheet: -2.80 (0.44), residues: 127 loop : -3.40 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a1021 HIS 0.005 0.001 HIS b 406 PHE 0.013 0.001 PHE b 83 TYR 0.021 0.002 TYR M3146 ARG 0.003 0.000 ARG a1347 *********************** 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 106 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.271 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 outliers start: 6 outliers final: 3 residues processed: 106 average time/residue: 0.5697 time to fit residues: 77.9851 Evaluate side-chains 97 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.307 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.2415 time to fit residues: 2.7087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 40.0000 chunk 88 optimal weight: 30.0000 chunk 80 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1075 ASN ** b 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.6792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7821 Z= 0.247 Angle : 0.662 6.979 10605 Z= 0.340 Chirality : 0.041 0.135 1159 Planarity : 0.005 0.076 1394 Dihedral : 6.251 80.274 1056 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.79 % Favored : 86.59 % Rotamer: Outliers : 0.96 % Allowed : 22.42 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.25), residues: 962 helix: -0.76 (0.23), residues: 460 sheet: -2.88 (0.43), residues: 132 loop : -3.23 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a1021 HIS 0.005 0.001 HIS b 406 PHE 0.010 0.001 PHE a1369 TYR 0.020 0.002 TYR M3146 ARG 0.003 0.000 ARG a1347 *********************** 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 106 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.388 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 outliers start: 8 outliers final: 5 residues processed: 105 average time/residue: 0.5759 time to fit residues: 78.4715 Evaluate side-chains 99 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.256 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 5 average time/residue: 0.2583 time to fit residues: 3.6234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 385 GLN M3166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7821 Z= 0.324 Angle : 0.700 7.647 10605 Z= 0.363 Chirality : 0.043 0.202 1159 Planarity : 0.006 0.072 1394 Dihedral : 6.357 75.352 1056 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.83 % Favored : 85.55 % Rotamer: Outliers : 0.60 % Allowed : 23.26 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.26), residues: 962 helix: -0.81 (0.24), residues: 453 sheet: -2.97 (0.44), residues: 127 loop : -3.17 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a1021 HIS 0.007 0.001 HIS b 406 PHE 0.021 0.002 PHE M3219 TYR 0.019 0.002 TYR b 312 ARG 0.005 0.001 ARG a1347 *********************** 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 97 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.240 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 outliers start: 5 outliers final: 4 residues processed: 96 average time/residue: 0.5685 time to fit residues: 70.7557 Evaluate side-chains 94 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 1.270 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.2453 time to fit residues: 3.0889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 40.0000 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.7028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7821 Z= 0.247 Angle : 0.661 7.388 10605 Z= 0.340 Chirality : 0.041 0.159 1159 Planarity : 0.005 0.073 1394 Dihedral : 6.130 70.250 1056 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.79 % Favored : 86.59 % Rotamer: Outliers : 0.36 % Allowed : 22.90 % Favored : 76.74 % 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: -2.86 (0.26), residues: 962 helix: -0.65 (0.24), residues: 451 sheet: -2.90 (0.45), residues: 127 loop : -3.04 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP a1021 HIS 0.005 0.001 HIS b 406 PHE 0.024 0.002 PHE M3219 TYR 0.017 0.002 TYR M3146 ARG 0.004 0.000 ARG a1347 ********************** 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 fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.361 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 outliers start: 3 outliers final: 3 residues processed: 93 average time/residue: 0.5457 time to fit residues: 66.5802 Evaluate side-chains 88 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 85 time to evaluate : 1.213 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.2411 time to fit residues: 2.7576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 6 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 = 0.3983 r_free = 0.3983 target = 0.099559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.079499 restraints weight = 61366.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.082104 restraints weight = 26891.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.083862 restraints weight = 16373.758| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.7199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7821 Z= 0.197 Angle : 0.634 7.251 10605 Z= 0.324 Chirality : 0.041 0.154 1159 Planarity : 0.005 0.072 1394 Dihedral : 5.814 63.306 1056 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.06 % Favored : 87.32 % Rotamer: Outliers : 0.36 % Allowed : 23.38 % Favored : 76.26 % 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: -2.66 (0.26), residues: 962 helix: -0.48 (0.24), residues: 460 sheet: -2.85 (0.46), residues: 127 loop : -2.97 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a1021 HIS 0.004 0.001 HIS b 406 PHE 0.020 0.001 PHE M3219 TYR 0.017 0.001 TYR M3146 ARG 0.003 0.000 ARG a1347 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.51 seconds wall clock time: 61 minutes 44.65 seconds (3704.65 seconds total)