Starting phenix.real_space_refine (version: dev) on Tue Dec 13 10:29:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kio_9996/12_2022/6kio_9996.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kio_9996/12_2022/6kio_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kio_9996/12_2022/6kio_9996.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kio_9996/12_2022/6kio_9996.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kio_9996/12_2022/6kio_9996.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kio_9996/12_2022/6kio_9996.pdb" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "b PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 39": "OD1" <-> "OD2" Residue "b ASP 41": "OD1" <-> "OD2" Residue "b GLU 47": "OE1" <-> "OE2" Residue "b TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 55": "OE1" <-> "OE2" Residue "b TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 90": "OD1" <-> "OD2" 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 113": "OE1" <-> "OE2" 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 GLU 160": "OE1" <-> "OE2" Residue "b TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 163": "OD1" <-> "OD2" Residue "b TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 196": "OE1" <-> "OE2" Residue "b ASP 199": "OD1" <-> "OD2" Residue "b GLU 200": "OE1" <-> "OE2" Residue "b GLU 207": "OE1" <-> "OE2" Residue "b TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b ASP 211": "OD1" <-> "OD2" 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 ASP 306": "OD1" <-> "OD2" Residue "b GLU 330": "OE1" <-> "OE2" Residue "b TYR 342": "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 GLU 386": "OE1" <-> "OE2" 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 TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 415": "OE1" <-> "OE2" Residue "b GLU 417": "OE1" <-> "OE2" Residue "b ASP 427": "OD1" <-> "OD2" Residue "b TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 3146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 3148": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 3153": "OD1" <-> "OD2" Residue "M ASP 3171": "OD1" <-> "OD2" Residue "M GLU 3185": "OE1" <-> "OE2" Residue "M GLU 3186": "OE1" <-> "OE2" Residue "M GLU 3187": "OE1" <-> "OE2" Residue "M ASP 3191": "OD1" <-> "OD2" Residue "M TYR 3196": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M GLU 3197": "OE1" <-> "OE2" Residue "a TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1027": "OE1" <-> "OE2" Residue "a PHE 1041": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 1043": "OD1" <-> "OD2" Residue "a GLU 1045": "OE1" <-> "OE2" Residue "a GLU 1051": "OE1" <-> "OE2" Residue "a TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1064": "OE1" <-> "OE2" Residue "a GLU 1071": "OE1" <-> "OE2" Residue "a ASP 1072": "OD1" <-> "OD2" 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 GLU 1087": "OE1" <-> "OE2" 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 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1129": "OE1" <-> "OE2" Residue "a ASP 1134": "OD1" <-> "OD2" Residue "a TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1142": "OE1" <-> "OE2" Residue "a TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1170": "OE1" <-> "OE2" Residue "a PHE 1176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a TYR 1184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1194": "OE1" <-> "OE2" Residue "a PHE 1218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1228": "OE1" <-> "OE2" 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 ASP 1280": "OD1" <-> "OD2" Residue "a TYR 1286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 1317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a ASP 1341": "OD1" <-> "OD2" Residue "a GLU 1360": "OE1" <-> "OE2" Residue "a PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1391": "OE1" <-> "OE2" Residue "a PHE 1392": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a GLU 1397": "OE1" <-> "OE2" Residue "a ASP 1405": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 7.40, per 1000 atoms: 0.49 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 - 3.50 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: 13.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1802 Finding SS restraints... Secondary structure from input PDB file: 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: 0.52 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: 5.92 Time building geometry restraints manager: 14.26 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: 83.95 - 95.69: 32 95.69 - 107.44: 4475 107.44 - 119.18: 16882 119.18 - 130.93: 6080 130.93 - 142.67: 39 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: 5497 18.96 - 37.91: 424 37.91 - 56.86: 148 56.86 - 75.81: 72 75.81 - 94.77: 25 Dihedral angle restraints: 6166 sinusoidal: 2841 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 6163 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 1.850 nonbonded pdb=" HG1 THR b 287 " pdb=" OE2 GLU b 290 " model vdw 1.543 1.850 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 1.850 ... (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 ========== 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 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. 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: 0.260 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: 0.220 Extract box with map and model: 2.840 Check model and map are aligned: 0.230 Convert atoms to be neutral: 0.150 Process input model: 53.740 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 7821 Z= 2.264 Angle : 3.432 21.130 10605 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 : 11.34 Ramachandran Plot: Outliers : 7.28 % Allowed : 18.61 % Favored : 74.12 % Rotamer Outliers : 8.39 % 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 *********************** 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 fitting. rotamer outliers: 70 poor density : 90 time to evaluate : 1.343 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 outliers start: 70 outliers final: 30 residues processed: 154 average time/residue: 0.4877 time to fit residues: 98.6700 Evaluate side-chains 110 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 80 time to evaluate : 1.348 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 3 residues processed: 30 average time/residue: 0.3274 time to fit residues: 15.6665 ------------------------------------------------------------------------------- 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: 5.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 337 ASN b 339 ASN b 433 GLN M3114 ASN M3155 GLN a1018 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 7821 Z= 0.310 Angle : 0.888 10.130 10605 Z= 0.484 Chirality : 0.045 0.164 1159 Planarity : 0.008 0.072 1394 Dihedral : 7.594 87.634 1056 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.27 % Favored : 87.11 % Rotamer Outliers : 2.28 % 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: -4.89 (0.22), residues: 962 helix: -3.07 (0.18), residues: 472 sheet: -2.71 (0.47), residues: 117 loop : -3.45 (0.26), residues: 373 *********************** 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 109 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 90 time to evaluate : 1.373 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 outliers start: 19 outliers final: 9 residues processed: 104 average time/residue: 0.5273 time to fit residues: 71.6863 Evaluate side-chains 89 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.435 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.3560 time to fit residues: 6.0480 ------------------------------------------------------------------------------- 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: 30.0000 chunk 27 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 94 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 281 GLN M3166 ASN a1075 ASN a1275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6193 moved from start: 0.4318 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= 0.194 Angle : 0.684 7.415 10605 Z= 0.363 Chirality : 0.041 0.147 1159 Planarity : 0.005 0.052 1394 Dihedral : 6.693 87.604 1056 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.00 % Favored : 91.37 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.24), residues: 962 helix: -2.11 (0.21), residues: 477 sheet: -2.06 (0.49), residues: 120 loop : -2.80 (0.29), residues: 365 *********************** 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 95 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 1.359 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 outliers start: 13 outliers final: 3 residues processed: 89 average time/residue: 0.5080 time to fit residues: 60.1816 Evaluate side-chains 78 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.323 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.1677 time to fit residues: 2.5435 ------------------------------------------------------------------------------- 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: 20.0000 chunk 45 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 59 ASN ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 HIS ** a1065 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1075 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 7821 Z= 0.290 Angle : 0.682 7.219 10605 Z= 0.360 Chirality : 0.041 0.145 1159 Planarity : 0.005 0.049 1394 Dihedral : 6.473 87.155 1056 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.52 % Favored : 90.96 % Rotamer Outliers : 1.44 % 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: -3.20 (0.25), residues: 962 helix: -1.70 (0.21), residues: 478 sheet: -1.86 (0.49), residues: 120 loop : -2.60 (0.30), residues: 364 *********************** 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 88 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.257 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 outliers start: 12 outliers final: 6 residues processed: 88 average time/residue: 0.5090 time to fit residues: 59.9005 Evaluate side-chains 80 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 1.370 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.1892 time to fit residues: 3.8382 ------------------------------------------------------------------------------- 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: 30.0000 chunk 1 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a1075 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6244 moved from start: 0.4958 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= 0.219 Angle : 0.634 6.784 10605 Z= 0.329 Chirality : 0.040 0.146 1159 Planarity : 0.004 0.049 1394 Dihedral : 6.194 86.978 1056 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.28 % Favored : 92.20 % Rotamer Outliers : 1.32 % 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: -2.65 (0.26), residues: 962 helix: -1.16 (0.23), residues: 475 sheet: -1.73 (0.48), residues: 120 loop : -2.42 (0.31), residues: 367 *********************** 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 86 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.456 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: 11 outliers final: 4 residues processed: 85 average time/residue: 0.5229 time to fit residues: 59.5157 Evaluate side-chains 76 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 1.383 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1776 time to fit residues: 2.8024 ------------------------------------------------------------------------------- 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: 20.0000 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 50.0000 chunk 22 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 48 optimal weight: 40.0000 chunk 89 optimal weight: 20.0000 overall best weight: 9.3990 ------------------------------------------------------------------------------- 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** a1075 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 7821 Z= 0.320 Angle : 0.672 7.509 10605 Z= 0.353 Chirality : 0.041 0.139 1159 Planarity : 0.004 0.049 1394 Dihedral : 6.251 86.585 1056 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.46 % Favored : 90.02 % Rotamer Outliers : 1.08 % 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: -2.54 (0.26), residues: 962 helix: -1.00 (0.23), residues: 472 sheet: -1.69 (0.49), residues: 120 loop : -2.46 (0.30), residues: 370 *********************** 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 80 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.148 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: 9 outliers final: 5 residues processed: 78 average time/residue: 0.4682 time to fit residues: 49.9988 Evaluate side-chains 74 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.318 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1914 time to fit residues: 3.2734 ------------------------------------------------------------------------------- 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: 20.0000 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 36 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M3214 ASN a1075 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7821 Z= 0.183 Angle : 0.599 6.288 10605 Z= 0.308 Chirality : 0.040 0.147 1159 Planarity : 0.004 0.046 1394 Dihedral : 5.937 86.608 1056 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.96 % Favored : 92.52 % Rotamer Outliers : 0.96 % 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: -2.05 (0.26), residues: 962 helix: -0.59 (0.24), residues: 472 sheet: -1.52 (0.50), residues: 120 loop : -2.22 (0.30), residues: 370 *********************** 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 82 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 1.312 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 outliers start: 8 outliers final: 4 residues processed: 81 average time/residue: 0.4689 time to fit residues: 51.6896 Evaluate side-chains 75 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 1.262 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1784 time to fit residues: 2.8505 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M3193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M3214 ASN a1107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 7821 Z= 0.223 Angle : 0.607 6.617 10605 Z= 0.314 Chirality : 0.040 0.142 1159 Planarity : 0.004 0.047 1394 Dihedral : 5.905 86.543 1056 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.21 % Favored : 91.37 % Rotamer Outliers : 0.60 % 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 (0.26), residues: 962 helix: -0.53 (0.23), residues: 471 sheet: -1.46 (0.50), residues: 120 loop : -2.15 (0.30), residues: 371 *********************** 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 74 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 1.384 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: 2 residues processed: 73 average time/residue: 0.4772 time to fit residues: 47.3123 Evaluate side-chains 71 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 1.284 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.4421 time to fit residues: 2.7049 ------------------------------------------------------------------------------- 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: 9.9990 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M3193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M3214 ASN ** a1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 7821 Z= 0.187 Angle : 0.591 6.314 10605 Z= 0.303 Chirality : 0.040 0.142 1159 Planarity : 0.004 0.046 1394 Dihedral : 5.757 86.434 1056 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.07 % Favored : 92.52 % Rotamer Outliers : 0.36 % 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: -1.70 (0.27), residues: 962 helix: -0.32 (0.24), residues: 471 sheet: -1.37 (0.51), residues: 120 loop : -2.01 (0.31), residues: 371 *********************** 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 75 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 1.343 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: 3 outliers final: 2 residues processed: 75 average time/residue: 0.4694 time to fit residues: 47.6546 Evaluate side-chains 70 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.222 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.1889 time to fit residues: 2.1768 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M3193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M3214 ASN ** a1223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7821 Z= 0.185 Angle : 0.595 7.211 10605 Z= 0.306 Chirality : 0.040 0.145 1159 Planarity : 0.004 0.045 1394 Dihedral : 5.677 86.175 1056 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.42 % Allowed : 7.90 % Favored : 91.68 % Rotamer Outliers : 0.12 % 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: -1.49 (0.27), residues: 962 helix: -0.16 (0.24), residues: 472 sheet: -1.23 (0.52), residues: 120 loop : -1.91 (0.31), residues: 370 ********************** 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 71 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 70 time to evaluate : 1.415 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: 1 outliers final: 1 residues processed: 71 average time/residue: 0.5022 time to fit residues: 48.3044 Evaluate side-chains 70 residues out of total 834 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.340 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1633 time to fit residues: 1.9716 ------------------------------------------------------------------------------- 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: 10.0000 chunk 70 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M3193 ASN ** 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 = 0.3681 r_free = 0.3681 target = 0.068987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.053459 restraints weight = 126079.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.054663 restraints weight = 61019.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.055329 restraints weight = 40253.651| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7821 Z= 0.175 Angle : 0.580 7.269 10605 Z= 0.297 Chirality : 0.040 0.142 1159 Planarity : 0.004 0.045 1394 Dihedral : 5.549 85.555 1056 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.86 % Favored : 92.72 % Rotamer Outliers : 0.12 % 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: -1.30 (0.28), residues: 962 helix: 0.07 (0.24), residues: 463 sheet: -1.48 (0.50), residues: 127 loop : -1.73 (0.32), residues: 372 =============================================================================== Job complete usr+sys time: 2736.65 seconds wall clock time: 49 minutes 40.01 seconds (2980.01 seconds total)