Starting phenix.real_space_refine on Mon Mar 25 10:56:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Bad SHEET records, were skipped: SHEET 1 AA1270 ILE A 23 ALA A 24 0 SHEET 3 AA1270 CYS A 49 THR A 57 -1 O LEU A 56 N LEU A 39 SHEET 5 AA1270 ILE A 104 ARG A 124 -1 O ILE A 106 N VAL A 98 SHEET 6 AA1270 LEU A 155 THR A 164 -1 O THR A 161 N ASN A 123 SHEET 8 AA1270 HIS A 186 ILE A 199 -1 O ARG A 195 N SER A 172 SHEET 10 AA1270 ASN A 221 HIS A 223 -1 O ASN A 221 N VAL A 213 SHEET 13 AA1270 CYS B 49 THR B 57 -1 O LEU B 56 N LEU B 39 SHEET 15 AA1270 ILE B 104 ARG B 124 -1 O ILE B 106 N VAL B 98 SHEET 16 AA1270 LEU B 155 THR B 164 -1 O THR B 161 N ASN B 123 SHEET 18 AA1270 HIS B 186 ILE B 199 -1 O ARG B 195 N SER B 172 SHEET 20 AA1270 ASN B 221 HIS B 223 -1 O ASN B 221 N VAL B 213 SHEET 23 AA1270 CYS C 49 THR C 57 -1 O LEU C 56 N LEU C 39 SHEET 25 AA1270 ILE C 104 ARG C 124 -1 O ILE C 106 N VAL C 98 SHEET 26 AA1270 LEU C 155 THR C 164 -1 O THR C 161 N ASN C 123 SHEET 28 AA1270 HIS C 186 ILE C 199 -1 O ARG C 195 N SER C 172 SHEET 30 AA1270 ASN C 221 HIS C 223 -1 O ASN C 221 N VAL C 213 SHEET 33 AA1270 CYS D 49 THR D 57 -1 O LEU D 56 N LEU D 39 SHEET 35 AA1270 ILE D 104 ARG D 124 -1 O GLN D 116 N ASP D 88 SHEET 36 AA1270 LEU D 155 THR D 164 -1 O THR D 161 N ASN D 123 SHEET 38 AA1270 HIS D 186 ILE D 199 -1 O ARG D 195 N SER D 172 SHEET 40 AA1270 ASN D 221 HIS D 223 -1 O ASN D 221 N VAL D 213 SHEET 43 AA1270 CYS E 49 THR E 57 -1 O LEU E 56 N LEU E 39 SHEET 45 AA1270 ILE E 104 ARG E 124 -1 O GLN E 116 N ASP E 88 SHEET 46 AA1270 LEU E 155 THR E 164 -1 O THR E 161 N ASN E 123 SHEET 48 AA1270 HIS E 186 ILE E 199 -1 O ARG E 195 N SER E 172 SHEET 50 AA1270 ASN E 221 HIS E 223 -1 O ASN E 221 N VAL E 213 SHEET 53 AA1270 CYS F 49 THR F 57 -1 O LEU F 56 N LEU F 39 SHEET 55 AA1270 ILE F 104 ARG F 124 -1 O GLN F 116 N ASP F 88 SHEET 56 AA1270 LEU F 155 THR F 164 -1 O THR F 161 N ASN F 123 SHEET 58 AA1270 HIS F 186 ILE F 199 -1 O ARG F 195 N SER F 172 SHEET 60 AA1270 ASN F 221 HIS F 223 -1 O ASN F 221 N VAL F 213 SHEET 63 AA1270 CYS G 49 THR G 57 -1 O LEU G 56 N LEU G 39 SHEET 65 AA1270 ILE G 104 ARG G 124 -1 O ILE G 106 N VAL G 98 SHEET 66 AA1270 LEU G 155 THR G 164 -1 O THR G 161 N ASN G 123 SHEET 68 AA1270 HIS G 186 ILE G 199 -1 O ARG G 195 N SER G 172 SHEET 70 AA1270 ASN G 221 HIS G 223 -1 O ASN G 221 N VAL G 213 SHEET 73 AA1270 CYS H 49 THR H 57 -1 O LEU H 56 N LEU H 39 SHEET 75 AA1270 ILE H 104 ARG H 124 -1 O ILE H 106 N VAL H 98 SHEET 76 AA1270 LEU H 155 THR H 164 -1 O THR H 161 N ASN H 123 SHEET 78 AA1270 HIS H 186 ILE H 199 -1 O ARG H 195 N SER H 172 SHEET 80 AA1270 ASN H 221 HIS H 223 -1 O ASN H 221 N VAL H 213 SHEET 83 AA1270 CYS I 49 THR I 57 -1 O LEU I 56 N LEU I 39 SHEET 85 AA1270 ILE I 104 ARG I 124 -1 O GLN I 116 N ASP I 88 SHEET 86 AA1270 LEU I 155 THR I 164 -1 O THR I 161 N ASN I 123 SHEET 88 AA1270 HIS I 186 ILE I 199 -1 O ARG I 195 N SER I 172 SHEET 90 AA1270 ASN I 221 HIS I 223 -1 O ASN I 221 N VAL I 213 SHEET 93 AA1270 CYS J 49 THR J 57 -1 O LEU J 56 N LEU J 39 SHEET 95 AA1270 ILE J 104 ARG J 124 -1 O GLN J 116 N ASP J 88 SHEET 96 AA1270 LEU J 155 THR J 164 -1 O THR J 161 N ASN J 123 SHEET 98 AA1270 HIS J 186 ILE J 199 -1 O ARG J 195 N SER J 172 SHEET 100 AA1270 ASN J 221 HIS J 223 -1 O ASN J 221 N VAL J 213 SHEET 103 AA1270 CYS K 49 THR K 57 -1 O LEU K 56 N LEU K 39 SHEET 105 AA1270 ILE K 104 ARG K 124 -1 O GLN K 116 N ASP K 88 SHEET 106 AA1270 LEU K 155 THR K 164 -1 O THR K 161 N ASN K 123 SHEET 108 AA1270 HIS K 186 ILE K 199 -1 O ARG K 195 N SER K 172 SHEET 110 AA1270 ASN K 221 HIS K 223 -1 O ASN K 221 N VAL K 213 SHEET 113 AA1270 CYS L 49 THR L 57 -1 O LEU L 56 N LEU L 39 SHEET 115 AA1270 ILE L 104 ARG L 124 -1 O ILE L 106 N VAL L 98 SHEET 116 AA1270 LEU L 155 THR L 164 -1 O THR L 161 N ASN L 123 SHEET 118 AA1270 HIS L 186 ILE L 199 -1 O ARG L 195 N SER L 172 SHEET 120 AA1270 ASN L 221 HIS L 223 -1 O ASN L 221 N VAL L 213 SHEET 123 AA1270 CYS M 49 THR M 57 -1 O LEU M 56 N LEU M 39 SHEET 125 AA1270 ILE M 104 ARG M 124 -1 O GLN M 116 N ASP M 88 SHEET 126 AA1270 LEU M 155 THR M 164 -1 O THR M 161 N ASN M 123 SHEET 128 AA1270 HIS M 186 ILE M 199 -1 O ARG M 195 N SER M 172 SHEET 130 AA1270 ASN M 221 HIS M 223 -1 O ASN M 221 N VAL M 213 SHEET 133 AA1270 CYS N 49 THR N 57 -1 O LEU N 56 N LEU N 39 SHEET 135 AA1270 ILE N 104 ARG N 124 -1 O ILE N 106 N VAL N 98 SHEET 136 AA1270 LEU N 155 THR N 164 -1 O THR N 161 N ASN N 123 SHEET 138 AA1270 HIS N 186 ILE N 199 -1 O ARG N 195 N SER N 172 SHEET 140 AA1270 ASN N 221 HIS N 223 -1 O ASN N 221 N VAL N 213 SHEET 143 AA1270 CYS O 49 THR O 57 -1 O LEU O 56 N LEU O 39 SHEET 145 AA1270 ILE O 104 ARG O 124 -1 O ILE O 106 N VAL O 98 SHEET 146 AA1270 LEU O 155 THR O 164 -1 O THR O 161 N ASN O 123 SHEET 148 AA1270 HIS O 186 ILE O 199 -1 O ARG O 195 N SER O 172 SHEET 150 AA1270 ASN O 221 HIS O 223 -1 O ASN O 221 N VAL O 213 SHEET 153 AA1270 CYS P 49 THR P 57 -1 O LEU P 56 N LEU P 39 SHEET 155 AA1270 ILE P 104 ARG P 124 -1 O GLN P 116 N ASP P 88 SHEET 156 AA1270 LEU P 155 THR P 164 -1 O THR P 161 N ASN P 123 SHEET 158 AA1270 HIS P 186 ILE P 199 -1 O ARG P 195 N SER P 172 SHEET 160 AA1270 ASN P 221 HIS P 223 -1 O ASN P 221 N VAL P 213 SHEET 163 AA1270 CYS Q 49 THR Q 57 -1 O LEU Q 56 N LEU Q 39 SHEET 165 AA1270 ILE Q 104 ARG Q 124 -1 O ILE Q 106 N VAL Q 98 SHEET 166 AA1270 LEU Q 155 THR Q 164 -1 O THR Q 161 N ASN Q 123 SHEET 168 AA1270 HIS Q 186 ILE Q 199 -1 O ARG Q 195 N SER Q 172 SHEET 170 AA1270 ASN Q 221 HIS Q 223 -1 O ASN Q 221 N VAL Q 213 SHEET 173 AA1270 CYS R 49 THR R 57 -1 O LEU R 56 N LEU R 39 SHEET 175 AA1270 ILE R 104 ARG R 124 -1 O GLN R 116 N ASP R 88 SHEET 176 AA1270 LEU R 155 THR R 164 -1 O THR R 161 N ASN R 123 SHEET 178 AA1270 HIS R 186 ILE R 199 -1 O ARG R 195 N SER R 172 SHEET 180 AA1270 ASN R 221 HIS R 223 -1 O ASN R 221 N VAL R 213 SHEET 183 AA1270 CYS S 49 THR S 57 -1 O LEU S 56 N LEU S 39 SHEET 185 AA1270 ILE S 104 ARG S 124 -1 O ILE S 106 N VAL S 98 SHEET 186 AA1270 LEU S 155 THR S 164 -1 O THR S 161 N ASN S 123 SHEET 188 AA1270 HIS S 186 ILE S 199 -1 O ARG S 195 N SER S 172 SHEET 190 AA1270 ASN S 221 HIS S 223 -1 O ASN S 221 N VAL S 213 SHEET 193 AA1270 CYS T 49 THR T 57 -1 O LEU T 56 N LEU T 39 SHEET 195 AA1270 ILE T 104 ARG T 124 -1 O GLN T 116 N ASP T 88 SHEET 196 AA1270 LEU T 155 THR T 164 -1 O THR T 161 N ASN T 123 SHEET 198 AA1270 HIS T 186 ILE T 199 -1 O ARG T 195 N SER T 172 SHEET 200 AA1270 ASN T 221 HIS T 223 -1 O ASN T 221 N VAL T 213 SHEET 203 AA1270 CYS V 49 THR V 57 -1 O LEU V 56 N LEU V 39 SHEET 205 AA1270 ILE V 104 ARG V 124 -1 O ILE V 106 N VAL V 98 SHEET 206 AA1270 LEU V 155 THR V 164 -1 O THR V 161 N ASN V 123 SHEET 208 AA1270 HIS V 186 ILE V 199 -1 O ARG V 195 N SER V 172 SHEET 210 AA1270 ASN V 221 HIS V 223 -1 O ASN V 221 N VAL V 213 SHEET 213 AA1270 CYS W 49 THR W 57 -1 O LEU W 56 N LEU W 39 SHEET 215 AA1270 ILE W 104 ARG W 124 -1 O ILE W 106 N VAL W 98 SHEET 216 AA1270 LEU W 155 THR W 164 -1 O THR W 161 N ASN W 123 SHEET 218 AA1270 HIS W 186 ILE W 199 -1 O ARG W 195 N SER W 172 SHEET 220 AA1270 ASN W 221 HIS W 223 -1 O ASN W 221 N VAL W 213 SHEET 223 AA1270 CYS X 49 THR X 57 -1 O LEU X 56 N LEU X 39 SHEET 225 AA1270 ILE X 104 ARG X 124 -1 O ILE X 106 N VAL X 98 SHEET 226 AA1270 LEU X 155 THR X 164 -1 O THR X 161 N ASN X 123 SHEET 228 AA1270 HIS X 186 ILE X 199 -1 O ARG X 195 N SER X 172 SHEET 230 AA1270 ASN X 221 HIS X 223 -1 O ASN X 221 N VAL X 213 SHEET 233 AA1270 CYS Y 49 THR Y 57 -1 O LEU Y 56 N LEU Y 39 SHEET 235 AA1270 ILE Y 104 ARG Y 124 -1 O ILE Y 106 N VAL Y 98 SHEET 236 AA1270 LEU Y 155 THR Y 164 -1 O THR Y 161 N ASN Y 123 SHEET 238 AA1270 HIS Y 186 ILE Y 199 -1 O ARG Y 195 N SER Y 172 SHEET 240 AA1270 ASN Y 221 HIS Y 223 -1 O ASN Y 221 N VAL Y 213 SHEET 243 AA1270 CYS Z 49 THR Z 57 -1 O LEU Z 56 N LEU Z 39 SHEET 245 AA1270 ILE Z 104 ARG Z 124 -1 O GLN Z 116 N ASP Z 88 SHEET 246 AA1270 LEU Z 155 THR Z 164 -1 O THR Z 161 N ASN Z 123 SHEET 248 AA1270 HIS Z 186 ILE Z 199 -1 O ARG Z 195 N SER Z 172 SHEET 250 AA1270 ASN Z 221 HIS Z 223 -1 O ASN Z 221 N VAL Z 213 SHEET 253 AA1270 CYSAA 49 THRAA 57 -1 O LEUAA 56 N LEUAA 39 SHEET 255 AA1270 ILEAA 104 ARGAA 124 -1 O GLNAA 116 N ASPAA 88 SHEET 256 AA1270 LEUAA 155 THRAA 164 -1 O THRAA 161 N ASNAA 123 SHEET 258 AA1270 HISAA 186 ILEAA 199 -1 O ARGAA 195 N SERAA 172 SHEET 260 AA1270 ASNAA 221 HISAA 223 -1 O ASNAA 221 N VALAA 213 SHEET 263 AA1270 CYSBA 49 THRBA 57 -1 O LEUBA 56 N LEUBA 39 SHEET 265 AA1270 ILEBA 104 ARGBA 124 -1 O ILEBA 106 N VALBA 98 SHEET 266 AA1270 LEUBA 155 THRBA 164 -1 O THRBA 161 N ASNBA 123 SHEET 268 AA1270 HISBA 186 ILEBA 199 -1 O ARGBA 195 N SERBA 172 SHEET 270 AA1270 ASNBA 221 HISBA 223 -1 O ASNBA 221 N VALBA 213 Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/03_2024/8gtn_34258.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/03_2024/8gtn_34258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/03_2024/8gtn_34258.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/03_2024/8gtn_34258.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/03_2024/8gtn_34258.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtn_34258/03_2024/8gtn_34258.pdb" } resolution = 3.17 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= -0.000 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 189 5.16 5 C 30753 2.51 5 N 8559 2.21 5 O 8802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AA PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 48303 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "X" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Z" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "AA" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "BA" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1789 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 6, 'TRANS': 210} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 23.00, per 1000 atoms: 0.48 Number of scatterers: 48303 At special positions: 0 Unit cell: (288.36, 288.36, 72.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 189 16.00 O 8802 8.00 N 8559 7.00 C 30753 6.00 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: 15.75 Conformation dependent library (CDL) restraints added in 7.9 seconds 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11070 Finding SS restraints... Bad SHEET records, were skipped: SHEET 1 AA1270 ILE A 23 ALA A 24 0 SHEET 3 AA1270 CYS A 49 THR A 57 -1 O LEU A 56 N LEU A 39 SHEET 5 AA1270 ILE A 104 ARG A 124 -1 O ILE A 106 N VAL A 98 SHEET 6 AA1270 LEU A 155 THR A 164 -1 O THR A 161 N ASN A 123 SHEET 8 AA1270 HIS A 186 ILE A 199 -1 O ARG A 195 N SER A 172 SHEET 10 AA1270 ASN A 221 HIS A 223 -1 O ASN A 221 N VAL A 213 SHEET 13 AA1270 CYS B 49 THR B 57 -1 O LEU B 56 N LEU B 39 SHEET 15 AA1270 ILE B 104 ARG B 124 -1 O ILE B 106 N VAL B 98 SHEET 16 AA1270 LEU B 155 THR B 164 -1 O THR B 161 N ASN B 123 SHEET 18 AA1270 HIS B 186 ILE B 199 -1 O ARG B 195 N SER B 172 SHEET 20 AA1270 ASN B 221 HIS B 223 -1 O ASN B 221 N VAL B 213 SHEET 23 AA1270 CYS C 49 THR C 57 -1 O LEU C 56 N LEU C 39 SHEET 25 AA1270 ILE C 104 ARG C 124 -1 O ILE C 106 N VAL C 98 SHEET 26 AA1270 LEU C 155 THR C 164 -1 O THR C 161 N ASN C 123 SHEET 28 AA1270 HIS C 186 ILE C 199 -1 O ARG C 195 N SER C 172 SHEET 30 AA1270 ASN C 221 HIS C 223 -1 O ASN C 221 N VAL C 213 SHEET 33 AA1270 CYS D 49 THR D 57 -1 O LEU D 56 N LEU D 39 SHEET 35 AA1270 ILE D 104 ARG D 124 -1 O GLN D 116 N ASP D 88 SHEET 36 AA1270 LEU D 155 THR D 164 -1 O THR D 161 N ASN D 123 SHEET 38 AA1270 HIS D 186 ILE D 199 -1 O ARG D 195 N SER D 172 SHEET 40 AA1270 ASN D 221 HIS D 223 -1 O ASN D 221 N VAL D 213 SHEET 43 AA1270 CYS E 49 THR E 57 -1 O LEU E 56 N LEU E 39 SHEET 45 AA1270 ILE E 104 ARG E 124 -1 O GLN E 116 N ASP E 88 SHEET 46 AA1270 LEU E 155 THR E 164 -1 O THR E 161 N ASN E 123 SHEET 48 AA1270 HIS E 186 ILE E 199 -1 O ARG E 195 N SER E 172 SHEET 50 AA1270 ASN E 221 HIS E 223 -1 O ASN E 221 N VAL E 213 SHEET 53 AA1270 CYS F 49 THR F 57 -1 O LEU F 56 N LEU F 39 SHEET 55 AA1270 ILE F 104 ARG F 124 -1 O GLN F 116 N ASP F 88 SHEET 56 AA1270 LEU F 155 THR F 164 -1 O THR F 161 N ASN F 123 SHEET 58 AA1270 HIS F 186 ILE F 199 -1 O ARG F 195 N SER F 172 SHEET 60 AA1270 ASN F 221 HIS F 223 -1 O ASN F 221 N VAL F 213 SHEET 63 AA1270 CYS G 49 THR G 57 -1 O LEU G 56 N LEU G 39 SHEET 65 AA1270 ILE G 104 ARG G 124 -1 O ILE G 106 N VAL G 98 SHEET 66 AA1270 LEU G 155 THR G 164 -1 O THR G 161 N ASN G 123 SHEET 68 AA1270 HIS G 186 ILE G 199 -1 O ARG G 195 N SER G 172 SHEET 70 AA1270 ASN G 221 HIS G 223 -1 O ASN G 221 N VAL G 213 SHEET 73 AA1270 CYS H 49 THR H 57 -1 O LEU H 56 N LEU H 39 SHEET 75 AA1270 ILE H 104 ARG H 124 -1 O ILE H 106 N VAL H 98 SHEET 76 AA1270 LEU H 155 THR H 164 -1 O THR H 161 N ASN H 123 SHEET 78 AA1270 HIS H 186 ILE H 199 -1 O ARG H 195 N SER H 172 SHEET 80 AA1270 ASN H 221 HIS H 223 -1 O ASN H 221 N VAL H 213 SHEET 83 AA1270 CYS I 49 THR I 57 -1 O LEU I 56 N LEU I 39 SHEET 85 AA1270 ILE I 104 ARG I 124 -1 O GLN I 116 N ASP I 88 SHEET 86 AA1270 LEU I 155 THR I 164 -1 O THR I 161 N ASN I 123 SHEET 88 AA1270 HIS I 186 ILE I 199 -1 O ARG I 195 N SER I 172 SHEET 90 AA1270 ASN I 221 HIS I 223 -1 O ASN I 221 N VAL I 213 SHEET 93 AA1270 CYS J 49 THR J 57 -1 O LEU J 56 N LEU J 39 SHEET 95 AA1270 ILE J 104 ARG J 124 -1 O GLN J 116 N ASP J 88 SHEET 96 AA1270 LEU J 155 THR J 164 -1 O THR J 161 N ASN J 123 SHEET 98 AA1270 HIS J 186 ILE J 199 -1 O ARG J 195 N SER J 172 SHEET 100 AA1270 ASN J 221 HIS J 223 -1 O ASN J 221 N VAL J 213 SHEET 103 AA1270 CYS K 49 THR K 57 -1 O LEU K 56 N LEU K 39 SHEET 105 AA1270 ILE K 104 ARG K 124 -1 O GLN K 116 N ASP K 88 SHEET 106 AA1270 LEU K 155 THR K 164 -1 O THR K 161 N ASN K 123 SHEET 108 AA1270 HIS K 186 ILE K 199 -1 O ARG K 195 N SER K 172 SHEET 110 AA1270 ASN K 221 HIS K 223 -1 O ASN K 221 N VAL K 213 SHEET 113 AA1270 CYS L 49 THR L 57 -1 O LEU L 56 N LEU L 39 SHEET 115 AA1270 ILE L 104 ARG L 124 -1 O ILE L 106 N VAL L 98 SHEET 116 AA1270 LEU L 155 THR L 164 -1 O THR L 161 N ASN L 123 SHEET 118 AA1270 HIS L 186 ILE L 199 -1 O ARG L 195 N SER L 172 SHEET 120 AA1270 ASN L 221 HIS L 223 -1 O ASN L 221 N VAL L 213 SHEET 123 AA1270 CYS M 49 THR M 57 -1 O LEU M 56 N LEU M 39 SHEET 125 AA1270 ILE M 104 ARG M 124 -1 O GLN M 116 N ASP M 88 SHEET 126 AA1270 LEU M 155 THR M 164 -1 O THR M 161 N ASN M 123 SHEET 128 AA1270 HIS M 186 ILE M 199 -1 O ARG M 195 N SER M 172 SHEET 130 AA1270 ASN M 221 HIS M 223 -1 O ASN M 221 N VAL M 213 SHEET 133 AA1270 CYS N 49 THR N 57 -1 O LEU N 56 N LEU N 39 SHEET 135 AA1270 ILE N 104 ARG N 124 -1 O ILE N 106 N VAL N 98 SHEET 136 AA1270 LEU N 155 THR N 164 -1 O THR N 161 N ASN N 123 SHEET 138 AA1270 HIS N 186 ILE N 199 -1 O ARG N 195 N SER N 172 SHEET 140 AA1270 ASN N 221 HIS N 223 -1 O ASN N 221 N VAL N 213 SHEET 143 AA1270 CYS O 49 THR O 57 -1 O LEU O 56 N LEU O 39 SHEET 145 AA1270 ILE O 104 ARG O 124 -1 O ILE O 106 N VAL O 98 SHEET 146 AA1270 LEU O 155 THR O 164 -1 O THR O 161 N ASN O 123 SHEET 148 AA1270 HIS O 186 ILE O 199 -1 O ARG O 195 N SER O 172 SHEET 150 AA1270 ASN O 221 HIS O 223 -1 O ASN O 221 N VAL O 213 SHEET 153 AA1270 CYS P 49 THR P 57 -1 O LEU P 56 N LEU P 39 SHEET 155 AA1270 ILE P 104 ARG P 124 -1 O GLN P 116 N ASP P 88 SHEET 156 AA1270 LEU P 155 THR P 164 -1 O THR P 161 N ASN P 123 SHEET 158 AA1270 HIS P 186 ILE P 199 -1 O ARG P 195 N SER P 172 SHEET 160 AA1270 ASN P 221 HIS P 223 -1 O ASN P 221 N VAL P 213 SHEET 163 AA1270 CYS Q 49 THR Q 57 -1 O LEU Q 56 N LEU Q 39 SHEET 165 AA1270 ILE Q 104 ARG Q 124 -1 O ILE Q 106 N VAL Q 98 SHEET 166 AA1270 LEU Q 155 THR Q 164 -1 O THR Q 161 N ASN Q 123 SHEET 168 AA1270 HIS Q 186 ILE Q 199 -1 O ARG Q 195 N SER Q 172 SHEET 170 AA1270 ASN Q 221 HIS Q 223 -1 O ASN Q 221 N VAL Q 213 SHEET 173 AA1270 CYS R 49 THR R 57 -1 O LEU R 56 N LEU R 39 SHEET 175 AA1270 ILE R 104 ARG R 124 -1 O GLN R 116 N ASP R 88 SHEET 176 AA1270 LEU R 155 THR R 164 -1 O THR R 161 N ASN R 123 SHEET 178 AA1270 HIS R 186 ILE R 199 -1 O ARG R 195 N SER R 172 SHEET 180 AA1270 ASN R 221 HIS R 223 -1 O ASN R 221 N VAL R 213 SHEET 183 AA1270 CYS S 49 THR S 57 -1 O LEU S 56 N LEU S 39 SHEET 185 AA1270 ILE S 104 ARG S 124 -1 O ILE S 106 N VAL S 98 SHEET 186 AA1270 LEU S 155 THR S 164 -1 O THR S 161 N ASN S 123 SHEET 188 AA1270 HIS S 186 ILE S 199 -1 O ARG S 195 N SER S 172 SHEET 190 AA1270 ASN S 221 HIS S 223 -1 O ASN S 221 N VAL S 213 SHEET 193 AA1270 CYS T 49 THR T 57 -1 O LEU T 56 N LEU T 39 SHEET 195 AA1270 ILE T 104 ARG T 124 -1 O GLN T 116 N ASP T 88 SHEET 196 AA1270 LEU T 155 THR T 164 -1 O THR T 161 N ASN T 123 SHEET 198 AA1270 HIS T 186 ILE T 199 -1 O ARG T 195 N SER T 172 SHEET 200 AA1270 ASN T 221 HIS T 223 -1 O ASN T 221 N VAL T 213 SHEET 203 AA1270 CYS V 49 THR V 57 -1 O LEU V 56 N LEU V 39 SHEET 205 AA1270 ILE V 104 ARG V 124 -1 O ILE V 106 N VAL V 98 SHEET 206 AA1270 LEU V 155 THR V 164 -1 O THR V 161 N ASN V 123 SHEET 208 AA1270 HIS V 186 ILE V 199 -1 O ARG V 195 N SER V 172 SHEET 210 AA1270 ASN V 221 HIS V 223 -1 O ASN V 221 N VAL V 213 SHEET 213 AA1270 CYS W 49 THR W 57 -1 O LEU W 56 N LEU W 39 SHEET 215 AA1270 ILE W 104 ARG W 124 -1 O ILE W 106 N VAL W 98 SHEET 216 AA1270 LEU W 155 THR W 164 -1 O THR W 161 N ASN W 123 SHEET 218 AA1270 HIS W 186 ILE W 199 -1 O ARG W 195 N SER W 172 SHEET 220 AA1270 ASN W 221 HIS W 223 -1 O ASN W 221 N VAL W 213 SHEET 223 AA1270 CYS X 49 THR X 57 -1 O LEU X 56 N LEU X 39 SHEET 225 AA1270 ILE X 104 ARG X 124 -1 O ILE X 106 N VAL X 98 SHEET 226 AA1270 LEU X 155 THR X 164 -1 O THR X 161 N ASN X 123 SHEET 228 AA1270 HIS X 186 ILE X 199 -1 O ARG X 195 N SER X 172 SHEET 230 AA1270 ASN X 221 HIS X 223 -1 O ASN X 221 N VAL X 213 SHEET 233 AA1270 CYS Y 49 THR Y 57 -1 O LEU Y 56 N LEU Y 39 SHEET 235 AA1270 ILE Y 104 ARG Y 124 -1 O ILE Y 106 N VAL Y 98 SHEET 236 AA1270 LEU Y 155 THR Y 164 -1 O THR Y 161 N ASN Y 123 SHEET 238 AA1270 HIS Y 186 ILE Y 199 -1 O ARG Y 195 N SER Y 172 SHEET 240 AA1270 ASN Y 221 HIS Y 223 -1 O ASN Y 221 N VAL Y 213 SHEET 243 AA1270 CYS Z 49 THR Z 57 -1 O LEU Z 56 N LEU Z 39 SHEET 245 AA1270 ILE Z 104 ARG Z 124 -1 O GLN Z 116 N ASP Z 88 SHEET 246 AA1270 LEU Z 155 THR Z 164 -1 O THR Z 161 N ASN Z 123 SHEET 248 AA1270 HIS Z 186 ILE Z 199 -1 O ARG Z 195 N SER Z 172 SHEET 250 AA1270 ASN Z 221 HIS Z 223 -1 O ASN Z 221 N VAL Z 213 SHEET 253 AA1270 CYSAA 49 THRAA 57 -1 O LEUAA 56 N LEUAA 39 SHEET 255 AA1270 ILEAA 104 ARGAA 124 -1 O GLNAA 116 N ASPAA 88 SHEET 256 AA1270 LEUAA 155 THRAA 164 -1 O THRAA 161 N ASNAA 123 SHEET 258 AA1270 HISAA 186 ILEAA 199 -1 O ARGAA 195 N SERAA 172 SHEET 260 AA1270 ASNAA 221 HISAA 223 -1 O ASNAA 221 N VALAA 213 SHEET 263 AA1270 CYSBA 49 THRBA 57 -1 O LEUBA 56 N LEUBA 39 SHEET 265 AA1270 ILEBA 104 ARGBA 124 -1 O ILEBA 106 N VALBA 98 SHEET 266 AA1270 LEUBA 155 THRBA 164 -1 O THRBA 161 N ASNBA 123 SHEET 268 AA1270 HISBA 186 ILEBA 199 -1 O ARGBA 195 N SERBA 172 SHEET 270 AA1270 ASNBA 221 HISBA 223 -1 O ASNBA 221 N VALBA 213 Secondary structure from input PDB file: 135 helices and 0 sheets defined 17.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG A 35 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU A 62 " --> pdb=" O MET A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 59 through 62' Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 143 through 148 Processing helix chain 'B' and resid 3 through 17 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG B 35 " --> pdb=" O ASP B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU B 62 " --> pdb=" O MET B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 59 through 62' Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'C' and resid 3 through 17 Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG C 35 " --> pdb=" O ASP C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU C 62 " --> pdb=" O MET C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 62' Processing helix chain 'C' and resid 126 through 133 Processing helix chain 'C' and resid 143 through 148 Processing helix chain 'D' and resid 3 through 17 Processing helix chain 'D' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG D 35 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU D 62 " --> pdb=" O MET D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 59 through 62' Processing helix chain 'D' and resid 126 through 133 Processing helix chain 'D' and resid 143 through 148 Processing helix chain 'E' and resid 3 through 17 Processing helix chain 'E' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG E 35 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU E 62 " --> pdb=" O MET E 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 59 through 62' Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'F' and resid 3 through 17 Processing helix chain 'F' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG F 35 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU F 62 " --> pdb=" O MET F 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 59 through 62' Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 143 through 148 Processing helix chain 'G' and resid 3 through 17 Processing helix chain 'G' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU G 62 " --> pdb=" O MET G 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 59 through 62' Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 143 through 148 Processing helix chain 'H' and resid 3 through 17 Processing helix chain 'H' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG H 35 " --> pdb=" O ASP H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU H 62 " --> pdb=" O MET H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 62' Processing helix chain 'H' and resid 126 through 133 Processing helix chain 'H' and resid 143 through 148 Processing helix chain 'I' and resid 3 through 17 Processing helix chain 'I' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG I 35 " --> pdb=" O ASP I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU I 62 " --> pdb=" O MET I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 59 through 62' Processing helix chain 'I' and resid 126 through 133 Processing helix chain 'I' and resid 143 through 148 Processing helix chain 'J' and resid 3 through 17 Processing helix chain 'J' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG J 35 " --> pdb=" O ASP J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU J 62 " --> pdb=" O MET J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 59 through 62' Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 143 through 148 Processing helix chain 'K' and resid 3 through 17 Processing helix chain 'K' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG K 35 " --> pdb=" O ASP K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU K 62 " --> pdb=" O MET K 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 59 through 62' Processing helix chain 'K' and resid 126 through 133 Processing helix chain 'K' and resid 143 through 148 Processing helix chain 'L' and resid 3 through 17 Processing helix chain 'L' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG L 35 " --> pdb=" O ASP L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU L 62 " --> pdb=" O MET L 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 59 through 62' Processing helix chain 'L' and resid 126 through 133 Processing helix chain 'L' and resid 143 through 148 Processing helix chain 'M' and resid 3 through 17 Processing helix chain 'M' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG M 35 " --> pdb=" O ASP M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU M 62 " --> pdb=" O MET M 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 59 through 62' Processing helix chain 'M' and resid 126 through 133 Processing helix chain 'M' and resid 143 through 148 Processing helix chain 'N' and resid 3 through 17 Processing helix chain 'N' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG N 35 " --> pdb=" O ASP N 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU N 62 " --> pdb=" O MET N 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 59 through 62' Processing helix chain 'N' and resid 126 through 133 Processing helix chain 'N' and resid 143 through 148 Processing helix chain 'O' and resid 3 through 17 Processing helix chain 'O' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG O 35 " --> pdb=" O ASP O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU O 62 " --> pdb=" O MET O 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 59 through 62' Processing helix chain 'O' and resid 126 through 133 Processing helix chain 'O' and resid 143 through 148 Processing helix chain 'P' and resid 3 through 17 Processing helix chain 'P' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG P 35 " --> pdb=" O ASP P 32 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU P 62 " --> pdb=" O MET P 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 59 through 62' Processing helix chain 'P' and resid 126 through 133 Processing helix chain 'P' and resid 143 through 148 Processing helix chain 'Q' and resid 3 through 17 Processing helix chain 'Q' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG Q 35 " --> pdb=" O ASP Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU Q 62 " --> pdb=" O MET Q 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 59 through 62' Processing helix chain 'Q' and resid 126 through 133 Processing helix chain 'Q' and resid 143 through 148 Processing helix chain 'R' and resid 3 through 17 Processing helix chain 'R' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG R 35 " --> pdb=" O ASP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU R 62 " --> pdb=" O MET R 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 59 through 62' Processing helix chain 'R' and resid 126 through 133 Processing helix chain 'R' and resid 143 through 148 Processing helix chain 'S' and resid 3 through 17 Processing helix chain 'S' and resid 31 through 35 removed outlier: 3.595A pdb=" N ARG S 35 " --> pdb=" O ASP S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 59 through 62 removed outlier: 3.710A pdb=" N LEU S 62 " --> pdb=" O MET S 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 59 through 62' Processing helix chain 'S' and resid 126 through 133 Processing helix chain 'S' and resid 143 through 148 Processing helix chain 'T' and resid 3 through 17 Processing helix chain 'T' and resid 31 through 35 removed outlier: 3.593A pdb=" N ARG T 35 " --> pdb=" O ASP T 32 " (cutoff:3.500A) Processing helix chain 'T' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU T 62 " --> pdb=" O MET T 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 59 through 62' Processing helix chain 'T' and resid 126 through 133 Processing helix chain 'T' and resid 143 through 148 Processing helix chain 'V' and resid 3 through 17 Processing helix chain 'V' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG V 35 " --> pdb=" O ASP V 32 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU V 62 " --> pdb=" O MET V 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 59 through 62' Processing helix chain 'V' and resid 126 through 133 Processing helix chain 'V' and resid 143 through 148 Processing helix chain 'W' and resid 3 through 17 Processing helix chain 'W' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG W 35 " --> pdb=" O ASP W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU W 62 " --> pdb=" O MET W 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 59 through 62' Processing helix chain 'W' and resid 126 through 133 Processing helix chain 'W' and resid 143 through 148 Processing helix chain 'X' and resid 3 through 17 Processing helix chain 'X' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG X 35 " --> pdb=" O ASP X 32 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU X 62 " --> pdb=" O MET X 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 59 through 62' Processing helix chain 'X' and resid 126 through 133 Processing helix chain 'X' and resid 143 through 148 Processing helix chain 'Y' and resid 3 through 17 Processing helix chain 'Y' and resid 31 through 35 removed outlier: 3.593A pdb=" N ARG Y 35 " --> pdb=" O ASP Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU Y 62 " --> pdb=" O MET Y 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 59 through 62' Processing helix chain 'Y' and resid 126 through 133 Processing helix chain 'Y' and resid 143 through 148 Processing helix chain 'Z' and resid 3 through 17 Processing helix chain 'Z' and resid 31 through 35 removed outlier: 3.594A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) Processing helix chain 'Z' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEU Z 62 " --> pdb=" O MET Z 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 59 through 62' Processing helix chain 'Z' and resid 126 through 133 Processing helix chain 'Z' and resid 143 through 148 Processing helix chain 'AA' and resid 3 through 17 Processing helix chain 'AA' and resid 31 through 35 removed outlier: 3.593A pdb=" N ARGAA 35 " --> pdb=" O ASPAA 32 " (cutoff:3.500A) Processing helix chain 'AA' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEUAA 62 " --> pdb=" O METAA 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'AA' and resid 59 through 62' Processing helix chain 'AA' and resid 126 through 133 Processing helix chain 'AA' and resid 143 through 148 Processing helix chain 'BA' and resid 3 through 17 Processing helix chain 'BA' and resid 31 through 35 removed outlier: 3.595A pdb=" N ARGBA 35 " --> pdb=" O ASPBA 32 " (cutoff:3.500A) Processing helix chain 'BA' and resid 59 through 62 removed outlier: 3.711A pdb=" N LEUBA 62 " --> pdb=" O METBA 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 59 through 62' Processing helix chain 'BA' and resid 126 through 133 Processing helix chain 'BA' and resid 143 through 148 486 hydrogen bonds defined for protein. 1377 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: 10.67 Time building geometry restraints manager: 17.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15795 1.34 - 1.46: 10574 1.46 - 1.58: 22528 1.58 - 1.69: 0 1.69 - 1.81: 324 Bond restraints: 49221 Sorted by residual: bond pdb=" N LEU H 100 " pdb=" CA LEU H 100 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.30e-02 5.92e+03 5.71e+00 bond pdb=" N LEU D 100 " pdb=" CA LEU D 100 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.30e-02 5.92e+03 5.64e+00 bond pdb=" N LEUBA 100 " pdb=" CA LEUBA 100 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.30e-02 5.92e+03 5.56e+00 bond pdb=" N LEU T 100 " pdb=" CA LEU T 100 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.30e-02 5.92e+03 5.52e+00 bond pdb=" N LEUAA 100 " pdb=" CA LEUAA 100 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.30e-02 5.92e+03 5.51e+00 ... (remaining 49216 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.12: 1027 107.12 - 113.82: 27611 113.82 - 120.52: 17965 120.52 - 127.22: 19061 127.22 - 133.93: 378 Bond angle restraints: 66042 Sorted by residual: angle pdb=" C LEU E 100 " pdb=" N PRO E 101 " pdb=" CA PRO E 101 " ideal model delta sigma weight residual 119.82 122.51 -2.69 9.80e-01 1.04e+00 7.53e+00 angle pdb=" C LEU V 100 " pdb=" N PRO V 101 " pdb=" CA PRO V 101 " ideal model delta sigma weight residual 119.82 122.51 -2.69 9.80e-01 1.04e+00 7.53e+00 angle pdb=" C LEU W 100 " pdb=" N PRO W 101 " pdb=" CA PRO W 101 " ideal model delta sigma weight residual 119.82 122.50 -2.68 9.80e-01 1.04e+00 7.51e+00 angle pdb=" C LEU S 100 " pdb=" N PRO S 101 " pdb=" CA PRO S 101 " ideal model delta sigma weight residual 119.82 122.50 -2.68 9.80e-01 1.04e+00 7.48e+00 angle pdb=" C LEU D 100 " pdb=" N PRO D 101 " pdb=" CA PRO D 101 " ideal model delta sigma weight residual 119.82 122.50 -2.68 9.80e-01 1.04e+00 7.47e+00 ... (remaining 66037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.39: 26002 11.39 - 22.78: 2732 22.78 - 34.17: 777 34.17 - 45.56: 189 45.56 - 56.95: 216 Dihedral angle restraints: 29916 sinusoidal: 12879 harmonic: 17037 Sorted by residual: dihedral pdb=" N ARG E 10 " pdb=" CA ARG E 10 " pdb=" CB ARG E 10 " pdb=" CG ARG E 10 " ideal model delta sinusoidal sigma weight residual -60.00 -116.95 56.95 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N ARG X 10 " pdb=" CA ARG X 10 " pdb=" CB ARG X 10 " pdb=" CG ARG X 10 " ideal model delta sinusoidal sigma weight residual -60.00 -116.94 56.94 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N ARG V 10 " pdb=" CA ARG V 10 " pdb=" CB ARG V 10 " pdb=" CG ARG V 10 " ideal model delta sinusoidal sigma weight residual -60.00 -116.94 56.94 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 29913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 5111 0.040 - 0.080: 1604 0.080 - 0.120: 469 0.120 - 0.160: 79 0.160 - 0.200: 27 Chirality restraints: 7290 Sorted by residual: chirality pdb=" CA LEU P 100 " pdb=" N LEU P 100 " pdb=" C LEU P 100 " pdb=" CB LEU P 100 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA LEU S 100 " pdb=" N LEU S 100 " pdb=" C LEU S 100 " pdb=" CB LEU S 100 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" CA LEU Z 100 " pdb=" N LEU Z 100 " pdb=" C LEU Z 100 " pdb=" CB LEU Z 100 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.92e-01 ... (remaining 7287 not shown) Planarity restraints: 8397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 200 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO H 201 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 201 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 201 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 200 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO F 201 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO F 201 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 201 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PROAA 200 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PROAA 201 " -0.058 5.00e-02 4.00e+02 pdb=" CA PROAA 201 " 0.017 5.00e-02 4.00e+02 pdb=" CD PROAA 201 " 0.018 5.00e-02 4.00e+02 ... (remaining 8394 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 5060 2.75 - 3.28: 49008 3.28 - 3.82: 79763 3.82 - 4.36: 98165 4.36 - 4.90: 168104 Nonbonded interactions: 400100 Sorted by model distance: nonbonded pdb=" O LEU R 212 " pdb=" OG SER R 230 " model vdw 2.208 2.440 nonbonded pdb=" O LEU X 212 " pdb=" OG SER X 230 " model vdw 2.208 2.440 nonbonded pdb=" O LEU C 212 " pdb=" OG SER C 230 " model vdw 2.208 2.440 nonbonded pdb=" O LEU Q 212 " pdb=" OG SER Q 230 " model vdw 2.208 2.440 nonbonded pdb=" O LEU H 212 " pdb=" OG SER H 230 " model vdw 2.208 2.440 ... (remaining 400095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'AA' selection = chain 'B' selection = chain 'BA' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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 individual isotropic 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: 6.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 30.150 Check model and map are aligned: 0.690 Set scattering table: 0.400 Process input model: 105.270 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.420 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 : 0.003 0.031 49221 Z= 0.209 Angle : 0.539 5.638 66042 Z= 0.308 Chirality : 0.043 0.200 7290 Planarity : 0.003 0.033 8397 Dihedral : 11.930 56.945 18846 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.50 % Allowed : 11.50 % Favored : 87.00 % 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: -1.98 (0.11), residues: 5751 helix: -1.14 (0.18), residues: 756 sheet: -1.79 (0.09), residues: 2538 loop : -0.51 (0.14), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 179 HIS 0.003 0.001 HISBA 186 PHE 0.012 0.001 PHE I 178 TYR 0.013 0.002 TYR L 176 ARG 0.002 0.000 ARG Q 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 872 time to evaluate : 5.826 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 111 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6780 (tm-30) REVERT: B 16 MET cc_start: 0.8121 (mmp) cc_final: 0.7861 (mmp) REVERT: B 187 LEU cc_start: 0.8826 (tt) cc_final: 0.8585 (mp) REVERT: C 170 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 178 PHE cc_start: 0.7381 (p90) cc_final: 0.6973 (p90) REVERT: C 189 TYR cc_start: 0.7466 (t80) cc_final: 0.7248 (t80) REVERT: D 16 MET cc_start: 0.8303 (mmp) cc_final: 0.8064 (mmt) REVERT: D 129 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.7040 (m-80) REVERT: D 178 PHE cc_start: 0.7427 (p90) cc_final: 0.6946 (p90) REVERT: D 189 TYR cc_start: 0.7320 (t80) cc_final: 0.6945 (t80) REVERT: E 16 MET cc_start: 0.8019 (mmp) cc_final: 0.7438 (mmt) REVERT: E 129 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.7008 (m-80) REVERT: E 179 TRP cc_start: 0.6790 (p90) cc_final: 0.6585 (p-90) REVERT: F 16 MET cc_start: 0.8407 (mmp) cc_final: 0.7848 (mmt) REVERT: G 16 MET cc_start: 0.8268 (mmp) cc_final: 0.7787 (mmt) REVERT: G 22 MET cc_start: 0.8509 (mtt) cc_final: 0.8073 (ttm) REVERT: G 129 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: G 178 PHE cc_start: 0.7605 (p90) cc_final: 0.7264 (p90) REVERT: G 179 TRP cc_start: 0.6732 (p90) cc_final: 0.6513 (p-90) REVERT: G 189 TYR cc_start: 0.7540 (t80) cc_final: 0.7299 (t80) REVERT: H 16 MET cc_start: 0.8049 (mmp) cc_final: 0.7634 (mmt) REVERT: I 16 MET cc_start: 0.8349 (mmp) cc_final: 0.7867 (mmp) REVERT: I 111 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6768 (tm-30) REVERT: K 146 PHE cc_start: 0.6292 (t80) cc_final: 0.6054 (t80) REVERT: L 110 PHE cc_start: 0.6935 (m-80) cc_final: 0.6723 (m-80) REVERT: L 129 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: M 16 MET cc_start: 0.8353 (mmp) cc_final: 0.7959 (mmp) REVERT: M 129 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: M 178 PHE cc_start: 0.7419 (p90) cc_final: 0.7193 (p90) REVERT: N 16 MET cc_start: 0.7854 (mmp) cc_final: 0.7413 (mmt) REVERT: N 110 PHE cc_start: 0.6721 (m-80) cc_final: 0.6491 (m-80) REVERT: N 129 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: N 187 LEU cc_start: 0.8777 (tt) cc_final: 0.8430 (mp) REVERT: O 16 MET cc_start: 0.7990 (mmp) cc_final: 0.7587 (mmt) REVERT: O 96 LEU cc_start: 0.8255 (pp) cc_final: 0.7924 (tt) REVERT: O 129 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6766 (m-80) REVERT: O 179 TRP cc_start: 0.6692 (p90) cc_final: 0.6468 (p-90) REVERT: P 60 ASP cc_start: 0.6724 (m-30) cc_final: 0.6494 (m-30) REVERT: P 129 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7081 (m-80) REVERT: Q 122 GLU cc_start: 0.7901 (tt0) cc_final: 0.7620 (pp20) REVERT: Q 129 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6791 (m-80) REVERT: R 16 MET cc_start: 0.8161 (mmp) cc_final: 0.7687 (mmp) REVERT: R 179 TRP cc_start: 0.6802 (p90) cc_final: 0.6570 (p-90) REVERT: S 16 MET cc_start: 0.8111 (mmp) cc_final: 0.7843 (mmt) REVERT: S 22 MET cc_start: 0.8420 (mtt) cc_final: 0.7975 (ttm) REVERT: T 16 MET cc_start: 0.8157 (mmp) cc_final: 0.7882 (mmp) REVERT: T 129 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: V 16 MET cc_start: 0.8000 (mmp) cc_final: 0.7527 (mmp) REVERT: V 129 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.7003 (m-80) REVERT: V 178 PHE cc_start: 0.7504 (p90) cc_final: 0.7291 (p90) REVERT: W 16 MET cc_start: 0.8148 (mmp) cc_final: 0.7797 (mmp) REVERT: W 178 PHE cc_start: 0.7542 (p90) cc_final: 0.7118 (p90) REVERT: W 189 TYR cc_start: 0.7465 (t80) cc_final: 0.7011 (t80) REVERT: X 16 MET cc_start: 0.8044 (mmp) cc_final: 0.7656 (mmt) REVERT: X 111 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: X 129 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: X 146 PHE cc_start: 0.6296 (t80) cc_final: 0.6072 (t80) REVERT: Y 16 MET cc_start: 0.8408 (mmp) cc_final: 0.7935 (mmt) REVERT: Y 111 GLN cc_start: 0.6924 (OUTLIER) cc_final: 0.6718 (tm-30) REVERT: Y 178 PHE cc_start: 0.7408 (p90) cc_final: 0.6910 (p90) REVERT: Y 189 TYR cc_start: 0.7484 (t80) cc_final: 0.7065 (t80) REVERT: Z 8 ILE cc_start: 0.8858 (tp) cc_final: 0.8644 (tp) REVERT: Z 96 LEU cc_start: 0.8121 (pp) cc_final: 0.7888 (tt) REVERT: Z 178 PHE cc_start: 0.7413 (p90) cc_final: 0.7082 (p90) REVERT: AA 16 MET cc_start: 0.8290 (mmp) cc_final: 0.7943 (mmt) REVERT: AA 22 MET cc_start: 0.8437 (mtt) cc_final: 0.8227 (ttm) REVERT: AA 129 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: BA 178 PHE cc_start: 0.7407 (p90) cc_final: 0.7041 (p90) outliers start: 81 outliers final: 17 residues processed: 953 average time/residue: 0.5715 time to fit residues: 908.8198 Evaluate side-chains 531 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 496 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain C residue 129 TYR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain E residue 129 TYR Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 129 TYR Chi-restraints excluded: chain J residue 129 TYR Chi-restraints excluded: chain K residue 129 TYR Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain M residue 129 TYR Chi-restraints excluded: chain N residue 129 TYR Chi-restraints excluded: chain O residue 129 TYR Chi-restraints excluded: chain P residue 129 TYR Chi-restraints excluded: chain Q residue 129 TYR Chi-restraints excluded: chain R residue 129 TYR Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 129 TYR Chi-restraints excluded: chain T residue 129 TYR Chi-restraints excluded: chain V residue 129 TYR Chi-restraints excluded: chain W residue 129 TYR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 129 TYR Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 129 TYR Chi-restraints excluded: chain Z residue 129 TYR Chi-restraints excluded: chain AA residue 129 TYR Chi-restraints excluded: chain BA residue 129 TYR Chi-restraints excluded: chain BA residue 170 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 478 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 289 optimal weight: 20.0000 chunk 229 optimal weight: 4.9990 chunk 444 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 270 optimal weight: 0.3980 chunk 330 optimal weight: 1.9990 chunk 514 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 186 HIS ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN B 175 GLN B 186 HIS ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN C 114 HIS C 186 HIS ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 GLN D 186 HIS ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 HIS G 111 GLN H 186 HIS ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 HIS J 111 GLN J 186 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 HIS ** K 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 HIS M 111 GLN N 111 GLN N 175 GLN N 186 HIS ** N 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 GLN O 175 GLN ** O 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 186 HIS ** P 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 186 HIS ** Q 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 HIS ** S 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 GLN T 175 GLN T 186 HIS V 111 GLN V 175 GLN V 186 HIS ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 186 HIS ** W 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 186 HIS ** X 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 175 GLN Y 186 HIS ** Y 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 186 HIS ** AA 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 111 GLN BA 175 GLN BA 186 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 49221 Z= 0.300 Angle : 0.612 8.120 66042 Z= 0.312 Chirality : 0.044 0.177 7290 Planarity : 0.004 0.035 8397 Dihedral : 5.784 48.526 6500 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.72 % Allowed : 15.63 % Favored : 82.65 % 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: -1.98 (0.11), residues: 5751 helix: -0.43 (0.20), residues: 621 sheet: -1.87 (0.09), residues: 2430 loop : -0.76 (0.13), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP M 179 HIS 0.004 0.001 HISBA 115 PHE 0.023 0.002 PHE K 47 TYR 0.014 0.002 TYR M 52 ARG 0.003 0.000 ARG S 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 520 time to evaluate : 5.668 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: C 16 MET cc_start: 0.8179 (mmp) cc_final: 0.7814 (mmt) REVERT: D 122 GLU cc_start: 0.7674 (pp20) cc_final: 0.7416 (pp20) REVERT: E 16 MET cc_start: 0.8199 (mmp) cc_final: 0.7460 (mmt) REVERT: H 16 MET cc_start: 0.8040 (mmp) cc_final: 0.7559 (mmt) REVERT: I 16 MET cc_start: 0.8443 (mmp) cc_final: 0.7861 (mmp) REVERT: I 168 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7171 (mm-30) REVERT: L 16 MET cc_start: 0.8272 (mmp) cc_final: 0.7964 (mmp) REVERT: L 110 PHE cc_start: 0.6954 (m-80) cc_final: 0.6711 (m-80) REVERT: M 16 MET cc_start: 0.8267 (mmp) cc_final: 0.7906 (mmt) REVERT: N 16 MET cc_start: 0.7834 (mmp) cc_final: 0.7366 (mmt) REVERT: N 110 PHE cc_start: 0.6860 (m-80) cc_final: 0.6634 (m-80) REVERT: N 129 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6782 (m-80) REVERT: O 110 PHE cc_start: 0.7049 (m-80) cc_final: 0.6826 (m-80) REVERT: P 60 ASP cc_start: 0.6639 (m-30) cc_final: 0.6434 (m-30) REVERT: R 179 TRP cc_start: 0.6813 (p90) cc_final: 0.6592 (p-90) REVERT: R 220 MET cc_start: 0.8446 (ttm) cc_final: 0.8206 (ttm) REVERT: S 16 MET cc_start: 0.8137 (mmp) cc_final: 0.7844 (mmt) REVERT: S 22 MET cc_start: 0.8584 (mtt) cc_final: 0.8154 (ttm) REVERT: T 16 MET cc_start: 0.8195 (mmp) cc_final: 0.7537 (mmt) REVERT: V 168 GLU cc_start: 0.7204 (mm-30) cc_final: 0.6990 (mm-30) REVERT: X 16 MET cc_start: 0.8116 (mmp) cc_final: 0.7602 (mmt) REVERT: Z 192 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8476 (tttp) REVERT: AA 122 GLU cc_start: 0.7512 (pp20) cc_final: 0.7257 (pp20) REVERT: AA 129 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: BA 16 MET cc_start: 0.8277 (mmp) cc_final: 0.7991 (mmt) REVERT: BA 178 PHE cc_start: 0.7475 (p90) cc_final: 0.7222 (p90) outliers start: 93 outliers final: 58 residues processed: 612 average time/residue: 0.5122 time to fit residues: 542.9755 Evaluate side-chains 504 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 443 time to evaluate : 5.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 129 TYR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 114 HIS Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 129 TYR Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 129 TYR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 129 TYR Chi-restraints excluded: chain J residue 129 TYR Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 129 TYR Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 129 TYR Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 129 TYR Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 129 TYR Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 129 TYR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 129 TYR Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 205 LEU Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain T residue 129 TYR Chi-restraints excluded: chain V residue 129 TYR Chi-restraints excluded: chain V residue 205 LEU Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 129 TYR Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 129 TYR Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 197 VAL Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 192 LYS Chi-restraints excluded: chain Z residue 205 LEU Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 129 TYR Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 286 optimal weight: 8.9990 chunk 159 optimal weight: 0.9980 chunk 428 optimal weight: 20.0000 chunk 350 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 515 optimal weight: 2.9990 chunk 557 optimal weight: 1.9990 chunk 459 optimal weight: 2.9990 chunk 511 optimal weight: 6.9990 chunk 175 optimal weight: 7.9990 chunk 413 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 114 HIS ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN C 194 GLN D 194 GLN E 111 GLN E 175 GLN E 194 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 GLN G 194 GLN H 194 GLN I 114 HIS I 194 GLN J 194 GLN ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 GLN ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 GLN M 194 GLN N 194 GLN O 194 GLN P 111 GLN P 175 GLN P 194 GLN ** Q 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 194 GLN R 111 GLN R 114 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 GLN R 194 GLN S 111 GLN S 175 GLN S 194 GLN T 194 GLN V 194 GLN W 111 GLN W 175 GLN W 194 GLN X 114 HIS X 194 GLN Y 194 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN AA 111 GLN AA 175 GLN AA 194 GLN ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 194 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 49221 Z= 0.344 Angle : 0.634 7.914 66042 Z= 0.326 Chirality : 0.044 0.148 7290 Planarity : 0.004 0.034 8397 Dihedral : 5.417 44.549 6462 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.28 % Allowed : 16.50 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.11), residues: 5751 helix: -0.33 (0.21), residues: 621 sheet: -1.91 (0.10), residues: 2430 loop : -0.94 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 179 HIS 0.015 0.002 HIS C 114 PHE 0.021 0.002 PHE Z 178 TYR 0.019 0.002 TYR M 52 ARG 0.003 0.000 ARG V 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 454 time to evaluate : 6.299 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: E 16 MET cc_start: 0.8172 (mmp) cc_final: 0.7416 (mmt) REVERT: F 16 MET cc_start: 0.8402 (mmp) cc_final: 0.8139 (mmp) REVERT: G 8 ILE cc_start: 0.8815 (tp) cc_final: 0.8595 (tp) REVERT: G 16 MET cc_start: 0.8438 (mmp) cc_final: 0.7708 (mmt) REVERT: I 111 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6285 (pp30) REVERT: L 11 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7851 (mp) REVERT: L 16 MET cc_start: 0.8310 (mmp) cc_final: 0.7806 (mmp) REVERT: M 16 MET cc_start: 0.8305 (mmp) cc_final: 0.7909 (mmt) REVERT: N 16 MET cc_start: 0.7872 (mmp) cc_final: 0.7358 (mmt) REVERT: P 60 ASP cc_start: 0.6751 (m-30) cc_final: 0.6532 (m-30) REVERT: P 168 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7220 (mm-30) REVERT: Q 16 MET cc_start: 0.8456 (mmp) cc_final: 0.7971 (mmt) REVERT: R 179 TRP cc_start: 0.6822 (p90) cc_final: 0.6599 (p-90) REVERT: S 11 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7766 (mp) REVERT: S 16 MET cc_start: 0.8210 (mmp) cc_final: 0.7832 (mmt) REVERT: S 22 MET cc_start: 0.8567 (mtt) cc_final: 0.8128 (ttm) REVERT: T 16 MET cc_start: 0.8212 (mmp) cc_final: 0.7476 (mmt) REVERT: W 11 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7740 (mp) REVERT: X 16 MET cc_start: 0.8206 (mmp) cc_final: 0.7611 (mmt) REVERT: Y 11 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7726 (mp) REVERT: Z 192 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8588 (tttp) REVERT: BA 8 ILE cc_start: 0.8839 (tp) cc_final: 0.8638 (tp) REVERT: BA 16 MET cc_start: 0.8333 (mmp) cc_final: 0.7939 (mmt) REVERT: BA 178 PHE cc_start: 0.7473 (p90) cc_final: 0.7220 (p90) outliers start: 177 outliers final: 99 residues processed: 628 average time/residue: 0.4978 time to fit residues: 558.4191 Evaluate side-chains 528 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 423 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 114 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 154 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 154 ASN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 154 ASN Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain R residue 114 HIS Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 154 ASN Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 205 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 158 VAL Chi-restraints excluded: chain V residue 158 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Y residue 197 VAL Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 154 ASN Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 192 LYS Chi-restraints excluded: chain Z residue 205 LEU Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 154 ASN Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 205 LEU Chi-restraints excluded: chain BA residue 87 LEU Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 154 ASN Chi-restraints excluded: chain BA residue 158 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 509 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 346 optimal weight: 0.8980 chunk 517 optimal weight: 4.9990 chunk 548 optimal weight: 0.7980 chunk 270 optimal weight: 0.5980 chunk 490 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 HIS ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS R 114 HIS T 114 HIS ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 114 HIS ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 49221 Z= 0.268 Angle : 0.588 8.259 66042 Z= 0.298 Chirality : 0.043 0.142 7290 Planarity : 0.004 0.033 8397 Dihedral : 4.556 15.691 6426 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.52 % Allowed : 19.39 % Favored : 78.09 % 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: -1.83 (0.11), residues: 5751 helix: -0.12 (0.21), residues: 621 sheet: -1.75 (0.10), residues: 2376 loop : -0.76 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 179 HIS 0.012 0.001 HIS B 114 PHE 0.020 0.002 PHE G 47 TYR 0.013 0.002 TYR H 176 ARG 0.004 0.000 ARG N 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 455 time to evaluate : 6.172 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 111 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: C 16 MET cc_start: 0.8218 (mmp) cc_final: 0.7858 (mmt) REVERT: C 110 PHE cc_start: 0.7243 (m-80) cc_final: 0.6916 (m-80) REVERT: D 16 MET cc_start: 0.8139 (mmp) cc_final: 0.7859 (mmt) REVERT: E 11 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7624 (mp) REVERT: F 16 MET cc_start: 0.8366 (mmp) cc_final: 0.8146 (mmp) REVERT: H 16 MET cc_start: 0.8058 (mmp) cc_final: 0.7571 (mmt) REVERT: I 16 MET cc_start: 0.8463 (mmp) cc_final: 0.7833 (mmp) REVERT: I 111 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6444 (pp30) REVERT: J 120 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8156 (pt) REVERT: J 205 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7695 (mp) REVERT: L 11 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7821 (mp) REVERT: L 16 MET cc_start: 0.8258 (mmp) cc_final: 0.7763 (mmp) REVERT: M 16 MET cc_start: 0.8223 (mmp) cc_final: 0.7888 (mmt) REVERT: N 16 MET cc_start: 0.7944 (mmp) cc_final: 0.7355 (mmt) REVERT: O 11 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7957 (mp) REVERT: Q 11 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7717 (mp) REVERT: Q 16 MET cc_start: 0.8398 (mmp) cc_final: 0.7948 (mmt) REVERT: R 179 TRP cc_start: 0.6877 (p90) cc_final: 0.6647 (p-90) REVERT: S 11 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7785 (mp) REVERT: S 16 MET cc_start: 0.8175 (mmp) cc_final: 0.7846 (mmt) REVERT: T 16 MET cc_start: 0.8167 (mmp) cc_final: 0.7444 (mmt) REVERT: T 231 PHE cc_start: 0.6231 (m-10) cc_final: 0.5967 (m-10) REVERT: W 11 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7744 (mp) REVERT: X 11 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7956 (mp) REVERT: X 16 MET cc_start: 0.8175 (mmp) cc_final: 0.7616 (mmt) REVERT: Y 11 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7727 (mp) REVERT: Y 111 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6504 (pp30) REVERT: Z 16 MET cc_start: 0.7994 (mmp) cc_final: 0.7596 (mmp) REVERT: Z 192 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8675 (tttp) REVERT: BA 8 ILE cc_start: 0.8876 (tp) cc_final: 0.8616 (tp) REVERT: BA 16 MET cc_start: 0.8337 (mmp) cc_final: 0.8006 (mmt) REVERT: BA 46 PHE cc_start: 0.4630 (m-10) cc_final: 0.4165 (m-10) REVERT: BA 118 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8463 (mm) REVERT: BA 178 PHE cc_start: 0.7451 (p90) cc_final: 0.7232 (p90) outliers start: 136 outliers final: 80 residues processed: 582 average time/residue: 0.4867 time to fit residues: 507.1652 Evaluate side-chains 523 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 428 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 58 LEU Chi-restraints excluded: chain L residue 114 HIS Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 154 ASN Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 154 ASN Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 154 ASN Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 114 HIS Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 154 ASN Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 154 ASN Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain V residue 205 LEU Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 197 VAL Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 154 ASN Chi-restraints excluded: chain Z residue 192 LYS Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 87 LEU Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 154 ASN Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 205 LEU Chi-restraints excluded: chain BA residue 87 LEU Chi-restraints excluded: chain BA residue 118 ILE Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 154 ASN Chi-restraints excluded: chain BA residue 158 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 456 optimal weight: 0.5980 chunk 311 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 408 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 467 optimal weight: 3.9990 chunk 378 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 279 optimal weight: 5.9990 chunk 491 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 111 GLN F 175 GLN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 114 HIS ** L 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 114 HIS ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 49221 Z= 0.357 Angle : 0.650 7.581 66042 Z= 0.331 Chirality : 0.045 0.163 7290 Planarity : 0.004 0.035 8397 Dihedral : 4.828 16.280 6426 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.19 % Allowed : 20.43 % Favored : 76.39 % 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: -2.00 (0.11), residues: 5751 helix: -0.10 (0.21), residues: 621 sheet: -1.84 (0.10), residues: 2376 loop : -0.95 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 179 HIS 0.010 0.002 HIS Q 114 PHE 0.021 0.002 PHEAA 178 TYR 0.020 0.002 TYR M 52 ARG 0.006 0.000 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 432 time to evaluate : 5.913 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 61 ILE cc_start: 0.6587 (OUTLIER) cc_final: 0.6225 (mm) REVERT: A 111 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7298 (pp30) REVERT: C 110 PHE cc_start: 0.7237 (m-80) cc_final: 0.6955 (m-80) REVERT: E 11 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7641 (mp) REVERT: F 16 MET cc_start: 0.8392 (mmp) cc_final: 0.8146 (mmp) REVERT: G 16 MET cc_start: 0.8423 (mmp) cc_final: 0.7717 (mmt) REVERT: H 16 MET cc_start: 0.8082 (mmp) cc_final: 0.7636 (mmt) REVERT: I 16 MET cc_start: 0.8442 (mmp) cc_final: 0.7787 (mmp) REVERT: I 61 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6429 (mm) REVERT: I 111 GLN cc_start: 0.7216 (OUTLIER) cc_final: 0.6541 (pp30) REVERT: J 16 MET cc_start: 0.8018 (mmp) cc_final: 0.7695 (mmt) REVERT: J 120 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8279 (pt) REVERT: L 11 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7847 (mp) REVERT: L 16 MET cc_start: 0.8254 (mmp) cc_final: 0.7552 (mmp) REVERT: L 46 PHE cc_start: 0.4515 (m-10) cc_final: 0.4143 (m-10) REVERT: M 16 MET cc_start: 0.8244 (mmp) cc_final: 0.7814 (mmt) REVERT: M 22 MET cc_start: 0.8542 (mtt) cc_final: 0.8150 (ttm) REVERT: N 16 MET cc_start: 0.7914 (mmp) cc_final: 0.7299 (mmt) REVERT: O 11 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7978 (mp) REVERT: P 46 PHE cc_start: 0.4646 (m-10) cc_final: 0.4308 (m-80) REVERT: Q 11 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7747 (mp) REVERT: Q 16 MET cc_start: 0.8422 (mmp) cc_final: 0.7953 (mmt) REVERT: R 16 MET cc_start: 0.7945 (mmp) cc_final: 0.7614 (mmt) REVERT: R 179 TRP cc_start: 0.6972 (p90) cc_final: 0.6683 (p-90) REVERT: S 11 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7777 (mp) REVERT: S 16 MET cc_start: 0.8159 (mmp) cc_final: 0.7845 (mmt) REVERT: S 136 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6331 (mtp180) REVERT: T 16 MET cc_start: 0.8164 (mmp) cc_final: 0.7508 (mmt) REVERT: T 231 PHE cc_start: 0.6241 (m-10) cc_final: 0.5979 (m-10) REVERT: V 61 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6636 (mm) REVERT: W 11 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7748 (mp) REVERT: X 11 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7959 (mp) REVERT: X 16 MET cc_start: 0.8203 (mmp) cc_final: 0.7594 (mmt) REVERT: Y 11 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7757 (mp) REVERT: Y 111 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6620 (pp30) REVERT: Z 61 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6640 (mm) REVERT: BA 8 ILE cc_start: 0.8943 (tp) cc_final: 0.8593 (tp) REVERT: BA 178 PHE cc_start: 0.7460 (p90) cc_final: 0.7184 (p90) outliers start: 172 outliers final: 116 residues processed: 599 average time/residue: 0.4798 time to fit residues: 519.8475 Evaluate side-chains 552 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 419 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 205 LEU Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 87 LEU Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain K residue 154 ASN Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 205 LEU Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 154 ASN Chi-restraints excluded: chain L residue 158 VAL Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain M residue 158 VAL Chi-restraints excluded: chain M residue 205 LEU Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 154 ASN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 154 ASN Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 154 ASN Chi-restraints excluded: chain P residue 158 VAL Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 154 ASN Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain S residue 154 ASN Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 205 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain V residue 158 VAL Chi-restraints excluded: chain V residue 205 LEU Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 154 ASN Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain W residue 205 LEU Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain X residue 158 VAL Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 154 ASN Chi-restraints excluded: chain Y residue 158 VAL Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 61 ILE Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 154 ASN Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 205 LEU Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 87 LEU Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 154 ASN Chi-restraints excluded: chain AA residue 158 VAL Chi-restraints excluded: chain AA residue 205 LEU Chi-restraints excluded: chain BA residue 87 LEU Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 154 ASN Chi-restraints excluded: chain BA residue 158 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 184 optimal weight: 10.0000 chunk 493 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 321 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 548 optimal weight: 0.5980 chunk 455 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 181 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 HIS ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 HIS ** X 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 211 GLN ** Z 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 49221 Z= 0.165 Angle : 0.517 7.510 66042 Z= 0.261 Chirality : 0.041 0.165 7290 Planarity : 0.003 0.035 8397 Dihedral : 4.091 14.977 6426 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.11 % Allowed : 22.06 % Favored : 75.83 % 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 (0.11), residues: 5751 helix: 0.12 (0.20), residues: 621 sheet: -1.49 (0.11), residues: 2376 loop : -0.57 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 179 HIS 0.004 0.001 HIS P 114 PHE 0.018 0.001 PHE W 178 TYR 0.007 0.001 TYR Y 176 ARG 0.005 0.000 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 517 time to evaluate : 6.079 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: B 61 ILE cc_start: 0.6778 (OUTLIER) cc_final: 0.6474 (mm) REVERT: C 16 MET cc_start: 0.8112 (mmp) cc_final: 0.7804 (mmt) REVERT: C 110 PHE cc_start: 0.7153 (m-80) cc_final: 0.6870 (m-80) REVERT: C 146 PHE cc_start: 0.6471 (t80) cc_final: 0.6269 (t80) REVERT: D 60 ASP cc_start: 0.6833 (m-30) cc_final: 0.6578 (m-30) REVERT: E 46 PHE cc_start: 0.5045 (m-10) cc_final: 0.4625 (m-10) REVERT: E 61 ILE cc_start: 0.6693 (OUTLIER) cc_final: 0.6349 (mm) REVERT: F 16 MET cc_start: 0.8290 (mmp) cc_final: 0.8079 (mmp) REVERT: F 231 PHE cc_start: 0.6293 (m-10) cc_final: 0.5976 (m-10) REVERT: G 22 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8165 (mtt) REVERT: H 16 MET cc_start: 0.8092 (mmp) cc_final: 0.7587 (mmt) REVERT: H 61 ILE cc_start: 0.7143 (OUTLIER) cc_final: 0.6902 (mm) REVERT: I 16 MET cc_start: 0.8395 (mmp) cc_final: 0.7788 (mmp) REVERT: J 16 MET cc_start: 0.7946 (mmp) cc_final: 0.7650 (mmt) REVERT: J 61 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6262 (mm) REVERT: J 120 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8175 (pt) REVERT: L 16 MET cc_start: 0.8210 (mmp) cc_final: 0.7875 (mmp) REVERT: L 46 PHE cc_start: 0.4407 (m-10) cc_final: 0.4036 (m-10) REVERT: L 61 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6526 (mm) REVERT: L 217 LYS cc_start: 0.8887 (mttt) cc_final: 0.8567 (mmtt) REVERT: M 16 MET cc_start: 0.8126 (mmp) cc_final: 0.7821 (mmt) REVERT: N 16 MET cc_start: 0.7883 (mmp) cc_final: 0.7272 (mmt) REVERT: O 11 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7990 (mp) REVERT: P 61 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6460 (mm) REVERT: Q 11 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7608 (mp) REVERT: R 16 MET cc_start: 0.7840 (mmp) cc_final: 0.7592 (mmt) REVERT: R 61 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6264 (mm) REVERT: R 179 TRP cc_start: 0.7026 (p90) cc_final: 0.5991 (p90) REVERT: R 220 MET cc_start: 0.7571 (ttm) cc_final: 0.7282 (ttm) REVERT: S 16 MET cc_start: 0.8180 (mmp) cc_final: 0.7875 (mmt) REVERT: S 62 LEU cc_start: 0.6880 (tp) cc_final: 0.6637 (tp) REVERT: T 16 MET cc_start: 0.8160 (mmp) cc_final: 0.7463 (mmt) REVERT: T 205 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7551 (mp) REVERT: W 11 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7682 (mp) REVERT: W 61 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6529 (mm) REVERT: X 11 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8006 (mt) REVERT: X 16 MET cc_start: 0.8059 (mmp) cc_final: 0.7690 (mmt) REVERT: Y 16 MET cc_start: 0.8189 (mmp) cc_final: 0.7670 (mmp) REVERT: Z 16 MET cc_start: 0.7821 (mmp) cc_final: 0.7474 (mmp) REVERT: AA 22 MET cc_start: 0.8525 (mtt) cc_final: 0.8234 (ttt) REVERT: AA 61 ILE cc_start: 0.6730 (OUTLIER) cc_final: 0.6357 (mm) REVERT: AA 146 PHE cc_start: 0.6950 (t80) cc_final: 0.6447 (t80) REVERT: BA 46 PHE cc_start: 0.5031 (m-10) cc_final: 0.4631 (m-10) REVERT: BA 61 ILE cc_start: 0.6745 (OUTLIER) cc_final: 0.6476 (mm) REVERT: BA 178 PHE cc_start: 0.7454 (p90) cc_final: 0.7206 (p90) outliers start: 114 outliers final: 54 residues processed: 628 average time/residue: 0.4612 time to fit residues: 526.0585 Evaluate side-chains 537 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 466 time to evaluate : 5.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 87 LEU Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 205 LEU Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 154 ASN Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 205 LEU Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain T residue 205 LEU Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 205 LEU Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Y residue 197 VAL Chi-restraints excluded: chain Y residue 205 LEU Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 13 VAL Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 205 LEU Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 528 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 312 optimal weight: 0.4980 chunk 400 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 461 optimal weight: 4.9990 chunk 306 optimal weight: 9.9990 chunk 546 optimal weight: 0.3980 chunk 342 optimal weight: 0.0370 chunk 333 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 211 GLN Y 114 HIS Z 111 GLN Z 175 GLN ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 49221 Z= 0.131 Angle : 0.495 8.014 66042 Z= 0.249 Chirality : 0.040 0.183 7290 Planarity : 0.003 0.033 8397 Dihedral : 3.748 14.969 6426 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.72 % Allowed : 23.33 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.11), residues: 5751 helix: 0.68 (0.20), residues: 594 sheet: -1.15 (0.11), residues: 2376 loop : -0.48 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 179 HIS 0.004 0.001 HIS S 186 PHE 0.017 0.001 PHE V 178 TYR 0.007 0.001 TYR P 189 ARG 0.005 0.000 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 586 time to evaluate : 6.222 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: B 59 MET cc_start: 0.7680 (mpp) cc_final: 0.7388 (mpp) REVERT: B 61 ILE cc_start: 0.6699 (OUTLIER) cc_final: 0.6490 (mm) REVERT: C 16 MET cc_start: 0.8060 (mmp) cc_final: 0.7759 (mmt) REVERT: C 96 LEU cc_start: 0.7421 (mp) cc_final: 0.7109 (tt) REVERT: C 110 PHE cc_start: 0.7036 (m-80) cc_final: 0.6825 (m-80) REVERT: D 16 MET cc_start: 0.7470 (mmt) cc_final: 0.7243 (mmt) REVERT: E 11 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7674 (mp) REVERT: E 16 MET cc_start: 0.8071 (mmp) cc_final: 0.7495 (mmt) REVERT: E 46 PHE cc_start: 0.5238 (m-10) cc_final: 0.4883 (m-10) REVERT: E 61 ILE cc_start: 0.6644 (OUTLIER) cc_final: 0.6340 (mm) REVERT: E 62 LEU cc_start: 0.6468 (tp) cc_final: 0.6207 (tp) REVERT: F 16 MET cc_start: 0.8161 (mmp) cc_final: 0.7946 (mmt) REVERT: F 231 PHE cc_start: 0.6106 (m-10) cc_final: 0.5865 (m-10) REVERT: G 22 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8036 (mtt) REVERT: H 16 MET cc_start: 0.8050 (mmp) cc_final: 0.7601 (mmt) REVERT: H 61 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6966 (mm) REVERT: I 16 MET cc_start: 0.8395 (mmp) cc_final: 0.7830 (mmp) REVERT: I 46 PHE cc_start: 0.4179 (m-10) cc_final: 0.3964 (m-10) REVERT: I 61 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6550 (mm) REVERT: J 16 MET cc_start: 0.7830 (mmp) cc_final: 0.7582 (mmt) REVERT: J 61 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6514 (mt) REVERT: J 62 LEU cc_start: 0.5969 (tp) cc_final: 0.5668 (tp) REVERT: J 220 MET cc_start: 0.7706 (ttm) cc_final: 0.7202 (ttm) REVERT: L 11 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7823 (mp) REVERT: L 16 MET cc_start: 0.8077 (mmp) cc_final: 0.7630 (mmt) REVERT: L 46 PHE cc_start: 0.4526 (m-10) cc_final: 0.4134 (m-10) REVERT: L 62 LEU cc_start: 0.6067 (tp) cc_final: 0.5852 (tp) REVERT: L 217 LYS cc_start: 0.8878 (mttt) cc_final: 0.8540 (mmtt) REVERT: M 16 MET cc_start: 0.8041 (mmp) cc_final: 0.7832 (mmt) REVERT: N 16 MET cc_start: 0.7824 (mmp) cc_final: 0.7391 (mmt) REVERT: N 61 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.6380 (mm) REVERT: O 11 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7987 (mp) REVERT: P 61 ILE cc_start: 0.7076 (OUTLIER) cc_final: 0.6655 (mm) REVERT: Q 11 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7594 (mp) REVERT: Q 16 MET cc_start: 0.8286 (mmp) cc_final: 0.7893 (mmt) REVERT: R 61 ILE cc_start: 0.6658 (OUTLIER) cc_final: 0.6177 (mm) REVERT: R 179 TRP cc_start: 0.7023 (p90) cc_final: 0.6031 (p90) REVERT: R 220 MET cc_start: 0.7857 (ttm) cc_final: 0.7576 (ttm) REVERT: S 11 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7828 (mp) REVERT: S 16 MET cc_start: 0.8055 (mmp) cc_final: 0.7850 (mmt) REVERT: S 217 LYS cc_start: 0.8946 (mttt) cc_final: 0.8613 (mmtt) REVERT: T 16 MET cc_start: 0.8100 (mmp) cc_final: 0.7453 (mmt) REVERT: X 11 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8003 (mt) REVERT: X 111 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: Y 11 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7684 (mp) REVERT: Y 16 MET cc_start: 0.8200 (mmp) cc_final: 0.7565 (mmt) REVERT: Z 16 MET cc_start: 0.7789 (mmp) cc_final: 0.7504 (mmp) REVERT: AA 22 MET cc_start: 0.8535 (mtt) cc_final: 0.8312 (ttt) REVERT: AA 61 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6450 (mm) REVERT: AA 62 LEU cc_start: 0.6372 (tp) cc_final: 0.6159 (tp) REVERT: AA 146 PHE cc_start: 0.6864 (t80) cc_final: 0.6389 (t80) REVERT: BA 46 PHE cc_start: 0.5337 (m-10) cc_final: 0.5071 (m-10) REVERT: BA 61 ILE cc_start: 0.6807 (OUTLIER) cc_final: 0.6581 (mm) outliers start: 93 outliers final: 48 residues processed: 674 average time/residue: 0.4640 time to fit residues: 570.1016 Evaluate side-chains 579 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 512 time to evaluate : 6.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 22 MET Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 154 ASN Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 154 ASN Chi-restraints excluded: chain P residue 61 ILE Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 154 ASN Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Y residue 197 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 154 ASN Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 53 THR Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 338 optimal weight: 2.9990 chunk 218 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 372 optimal weight: 4.9990 chunk 270 optimal weight: 0.6980 chunk 50 optimal weight: 20.0000 chunk 429 optimal weight: 10.0000 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 111 GLN K 175 GLN L 111 GLN ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 114 HIS ** S 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 49221 Z= 0.390 Angle : 0.670 12.568 66042 Z= 0.341 Chirality : 0.045 0.148 7290 Planarity : 0.004 0.036 8397 Dihedral : 4.702 18.870 6426 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.81 % Allowed : 23.57 % Favored : 73.61 % 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: -1.66 (0.11), residues: 5751 helix: 0.11 (0.21), residues: 621 sheet: -1.52 (0.11), residues: 2376 loop : -0.81 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 179 HIS 0.005 0.002 HIS B 115 PHE 0.021 0.002 PHE V 178 TYR 0.023 0.003 TYR M 52 ARG 0.006 0.000 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 477 time to evaluate : 5.966 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: B 61 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6431 (mm) REVERT: C 16 MET cc_start: 0.8217 (mmp) cc_final: 0.7812 (mmt) REVERT: C 96 LEU cc_start: 0.7411 (mp) cc_final: 0.7102 (tt) REVERT: C 110 PHE cc_start: 0.7175 (m-80) cc_final: 0.6957 (m-80) REVERT: D 16 MET cc_start: 0.8085 (mmt) cc_final: 0.7486 (mmt) REVERT: E 11 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7670 (mp) REVERT: E 46 PHE cc_start: 0.5178 (m-10) cc_final: 0.4812 (m-10) REVERT: E 61 ILE cc_start: 0.6553 (OUTLIER) cc_final: 0.6230 (mm) REVERT: F 16 MET cc_start: 0.8386 (mmp) cc_final: 0.8144 (mmp) REVERT: F 96 LEU cc_start: 0.7723 (mp) cc_final: 0.7259 (tt) REVERT: F 231 PHE cc_start: 0.6292 (m-10) cc_final: 0.5982 (m-10) REVERT: G 16 MET cc_start: 0.8143 (mmt) cc_final: 0.7520 (mmt) REVERT: H 16 MET cc_start: 0.8108 (mmp) cc_final: 0.7535 (mmt) REVERT: H 61 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6989 (mm) REVERT: H 110 PHE cc_start: 0.6927 (m-80) cc_final: 0.6685 (m-80) REVERT: I 16 MET cc_start: 0.8489 (mmp) cc_final: 0.7788 (mmp) REVERT: I 46 PHE cc_start: 0.4194 (m-10) cc_final: 0.3953 (m-10) REVERT: I 61 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6493 (mm) REVERT: J 120 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8170 (pt) REVERT: K 16 MET cc_start: 0.8320 (mmp) cc_final: 0.8087 (mmp) REVERT: L 11 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7811 (mp) REVERT: L 46 PHE cc_start: 0.4579 (m-10) cc_final: 0.4156 (m-10) REVERT: L 217 LYS cc_start: 0.8902 (mttt) cc_final: 0.8568 (mmtt) REVERT: M 16 MET cc_start: 0.8258 (mmp) cc_final: 0.7771 (mmt) REVERT: M 22 MET cc_start: 0.8560 (mtt) cc_final: 0.8190 (ttm) REVERT: N 61 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6484 (mm) REVERT: O 11 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7924 (mp) REVERT: Q 11 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7720 (mp) REVERT: Q 16 MET cc_start: 0.8427 (mmp) cc_final: 0.7962 (mmt) REVERT: R 61 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6066 (mm) REVERT: R 179 TRP cc_start: 0.6991 (p90) cc_final: 0.6701 (p-90) REVERT: R 220 MET cc_start: 0.7990 (ttm) cc_final: 0.7684 (ttm) REVERT: S 11 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7768 (mp) REVERT: S 16 MET cc_start: 0.8085 (mmp) cc_final: 0.7808 (mmt) REVERT: S 136 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6287 (mtp180) REVERT: T 16 MET cc_start: 0.8187 (mmp) cc_final: 0.7506 (mmt) REVERT: W 11 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7748 (mp) REVERT: X 11 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.7939 (mp) REVERT: X 46 PHE cc_start: 0.4934 (m-10) cc_final: 0.4706 (m-10) REVERT: Y 11 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7734 (mp) REVERT: Y 111 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7040 (pp30) REVERT: Z 16 MET cc_start: 0.7892 (mmp) cc_final: 0.7493 (mmp) REVERT: AA 61 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6559 (mm) REVERT: BA 16 MET cc_start: 0.7498 (mmt) cc_final: 0.7123 (mmm) REVERT: BA 46 PHE cc_start: 0.5171 (m-10) cc_final: 0.4779 (m-10) REVERT: BA 61 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6568 (mm) outliers start: 152 outliers final: 98 residues processed: 626 average time/residue: 0.4702 time to fit residues: 533.6643 Evaluate side-chains 581 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 464 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 114 HIS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 87 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain I residue 154 ASN Chi-restraints excluded: chain I residue 158 VAL Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 120 ILE Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 154 ASN Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 154 ASN Chi-restraints excluded: chain P residue 13 VAL Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 154 ASN Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 154 ASN Chi-restraints excluded: chain Q residue 158 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 13 VAL Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain S residue 136 ARG Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain T residue 120 ILE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 120 ILE Chi-restraints excluded: chain V residue 222 ILE Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 87 LEU Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain W residue 228 THR Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 120 ILE Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 154 ASN Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 13 VAL Chi-restraints excluded: chain AA residue 53 THR Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain AA residue 154 ASN Chi-restraints excluded: chain BA residue 11 ILE Chi-restraints excluded: chain BA residue 13 VAL Chi-restraints excluded: chain BA residue 53 THR Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 154 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 497 optimal weight: 0.6980 chunk 523 optimal weight: 3.9990 chunk 477 optimal weight: 0.9990 chunk 509 optimal weight: 0.9990 chunk 306 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 399 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 460 optimal weight: 3.9990 chunk 481 optimal weight: 0.9990 chunk 507 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 49221 Z= 0.179 Angle : 0.546 8.572 66042 Z= 0.275 Chirality : 0.042 0.195 7290 Planarity : 0.003 0.033 8397 Dihedral : 4.166 17.746 6426 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.31 % Allowed : 24.41 % Favored : 73.28 % 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: -1.26 (0.11), residues: 5751 helix: 0.52 (0.20), residues: 594 sheet: -1.26 (0.11), residues: 2376 loop : -0.57 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 179 HIS 0.015 0.001 HIS A 114 PHE 0.018 0.001 PHE V 178 TYR 0.009 0.001 TYR M 52 ARG 0.005 0.000 ARG O 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 509 time to evaluate : 6.270 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: A 110 PHE cc_start: 0.6948 (m-80) cc_final: 0.6511 (m-80) REVERT: B 61 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6510 (mm) REVERT: C 16 MET cc_start: 0.8139 (mmp) cc_final: 0.7813 (mmt) REVERT: C 96 LEU cc_start: 0.7331 (mp) cc_final: 0.7074 (tt) REVERT: C 110 PHE cc_start: 0.7092 (m-80) cc_final: 0.6878 (m-80) REVERT: D 16 MET cc_start: 0.7883 (mmt) cc_final: 0.7561 (mmt) REVERT: E 11 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7567 (mp) REVERT: E 46 PHE cc_start: 0.5230 (m-10) cc_final: 0.4872 (m-10) REVERT: E 61 ILE cc_start: 0.6633 (OUTLIER) cc_final: 0.6275 (mm) REVERT: F 16 MET cc_start: 0.8284 (mmp) cc_final: 0.8010 (mmt) REVERT: F 96 LEU cc_start: 0.7661 (mp) cc_final: 0.7211 (tt) REVERT: F 231 PHE cc_start: 0.6213 (m-10) cc_final: 0.5946 (m-10) REVERT: G 16 MET cc_start: 0.8049 (mmt) cc_final: 0.7628 (mmt) REVERT: I 16 MET cc_start: 0.8423 (mmp) cc_final: 0.7823 (mmp) REVERT: I 46 PHE cc_start: 0.4225 (m-10) cc_final: 0.3996 (m-10) REVERT: I 61 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6453 (mm) REVERT: J 16 MET cc_start: 0.7983 (mmp) cc_final: 0.7648 (mmt) REVERT: L 11 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7814 (mp) REVERT: L 46 PHE cc_start: 0.4513 (m-10) cc_final: 0.4131 (m-10) REVERT: L 217 LYS cc_start: 0.8885 (mttt) cc_final: 0.8575 (mmtt) REVERT: M 16 MET cc_start: 0.8032 (mmp) cc_final: 0.7712 (mmt) REVERT: N 16 MET cc_start: 0.7916 (mmp) cc_final: 0.7289 (mmt) REVERT: N 61 ILE cc_start: 0.6700 (OUTLIER) cc_final: 0.6441 (mm) REVERT: O 11 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7984 (mp) REVERT: Q 11 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7612 (mp) REVERT: R 61 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6221 (mm) REVERT: R 179 TRP cc_start: 0.6947 (p90) cc_final: 0.5879 (p90) REVERT: R 220 MET cc_start: 0.7937 (ttm) cc_final: 0.7711 (ttm) REVERT: S 11 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7793 (mp) REVERT: S 16 MET cc_start: 0.8134 (mmp) cc_final: 0.7805 (mmt) REVERT: T 16 MET cc_start: 0.8159 (mmp) cc_final: 0.7547 (mmp) REVERT: T 96 LEU cc_start: 0.7677 (mp) cc_final: 0.7250 (tt) REVERT: W 11 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7694 (mp) REVERT: X 11 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7896 (mp) REVERT: X 46 PHE cc_start: 0.4931 (m-10) cc_final: 0.4704 (m-10) REVERT: X 111 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: Y 16 MET cc_start: 0.8214 (mmp) cc_final: 0.7612 (mmt) REVERT: Z 16 MET cc_start: 0.7786 (mmp) cc_final: 0.7550 (mmp) REVERT: AA 22 MET cc_start: 0.8533 (mtt) cc_final: 0.8260 (ttt) REVERT: AA 61 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6385 (mm) REVERT: AA 62 LEU cc_start: 0.6424 (tp) cc_final: 0.6175 (tp) REVERT: AA 146 PHE cc_start: 0.6844 (t80) cc_final: 0.6475 (t80) REVERT: BA 46 PHE cc_start: 0.5418 (m-10) cc_final: 0.5094 (m-10) REVERT: BA 61 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6561 (mm) outliers start: 125 outliers final: 76 residues processed: 630 average time/residue: 0.4693 time to fit residues: 536.5898 Evaluate side-chains 582 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 491 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 154 ASN Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 120 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain M residue 11 ILE Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 120 ILE Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 154 ASN Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 13 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 154 ASN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain R residue 154 ASN Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain T residue 53 THR Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain Y residue 13 VAL Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 58 LEU Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 154 ASN Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 13 VAL Chi-restraints excluded: chain AA residue 53 THR Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain AA residue 120 ILE Chi-restraints excluded: chain BA residue 22 MET Chi-restraints excluded: chain BA residue 53 THR Chi-restraints excluded: chain BA residue 61 ILE Chi-restraints excluded: chain BA residue 120 ILE Chi-restraints excluded: chain BA residue 154 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 334 optimal weight: 0.9990 chunk 538 optimal weight: 5.9990 chunk 328 optimal weight: 4.9990 chunk 255 optimal weight: 0.1980 chunk 374 optimal weight: 4.9990 chunk 564 optimal weight: 0.6980 chunk 519 optimal weight: 0.0980 chunk 449 optimal weight: 0.0570 chunk 46 optimal weight: 5.9990 chunk 347 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 overall best weight: 0.4100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** G 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** Z 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 49221 Z= 0.132 Angle : 0.504 8.584 66042 Z= 0.254 Chirality : 0.041 0.142 7290 Planarity : 0.003 0.032 8397 Dihedral : 3.739 19.051 6426 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.57 % Allowed : 25.41 % Favored : 73.02 % 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: -0.99 (0.11), residues: 5751 helix: 0.72 (0.20), residues: 594 sheet: -0.99 (0.11), residues: 2376 loop : -0.50 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPAA 179 HIS 0.005 0.001 HIS G 114 PHE 0.018 0.001 PHEAA 178 TYR 0.006 0.001 TYR P 189 ARG 0.004 0.000 ARG O 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11502 Ramachandran restraints generated. 5751 Oldfield, 0 Emsley, 5751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 566 time to evaluate : 5.991 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METAA 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "METBA 1 " (corrupted residue). Skipping it. REVERT: B 16 MET cc_start: 0.7886 (mmp) cc_final: 0.7645 (mmp) REVERT: C 16 MET cc_start: 0.8014 (mmp) cc_final: 0.7765 (mmt) REVERT: C 96 LEU cc_start: 0.7233 (mp) cc_final: 0.7020 (tt) REVERT: C 110 PHE cc_start: 0.7068 (m-80) cc_final: 0.6847 (m-80) REVERT: D 16 MET cc_start: 0.7715 (mmt) cc_final: 0.7299 (mmt) REVERT: D 59 MET cc_start: 0.7767 (mpp) cc_final: 0.7564 (mpp) REVERT: E 11 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7498 (mp) REVERT: E 46 PHE cc_start: 0.5446 (m-10) cc_final: 0.5096 (m-10) REVERT: E 61 ILE cc_start: 0.6549 (OUTLIER) cc_final: 0.6149 (mm) REVERT: F 16 MET cc_start: 0.8215 (mmp) cc_final: 0.7852 (mmt) REVERT: F 231 PHE cc_start: 0.6198 (m-10) cc_final: 0.5931 (m-10) REVERT: G 16 MET cc_start: 0.7922 (mmt) cc_final: 0.7503 (mmt) REVERT: G 194 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7550 (tm-30) REVERT: H 16 MET cc_start: 0.8039 (mmp) cc_final: 0.7623 (mmt) REVERT: I 16 MET cc_start: 0.8392 (mmp) cc_final: 0.7860 (mmp) REVERT: I 46 PHE cc_start: 0.4188 (m-10) cc_final: 0.3943 (m-10) REVERT: I 61 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6466 (mm) REVERT: J 96 LEU cc_start: 0.7691 (mp) cc_final: 0.7429 (tt) REVERT: L 11 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7728 (mp) REVERT: L 16 MET cc_start: 0.7673 (mmp) cc_final: 0.7265 (mmm) REVERT: L 46 PHE cc_start: 0.4474 (m-10) cc_final: 0.4099 (m-10) REVERT: M 16 MET cc_start: 0.7900 (mmp) cc_final: 0.7700 (mmt) REVERT: N 16 MET cc_start: 0.7785 (mmp) cc_final: 0.7348 (mmt) REVERT: O 11 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7966 (mp) REVERT: Q 11 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7600 (mp) REVERT: R 179 TRP cc_start: 0.6993 (p90) cc_final: 0.5907 (p90) REVERT: S 11 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7774 (mp) REVERT: S 16 MET cc_start: 0.8015 (mmp) cc_final: 0.7805 (mmt) REVERT: T 16 MET cc_start: 0.8089 (mmp) cc_final: 0.7537 (mmp) REVERT: T 96 LEU cc_start: 0.7695 (mp) cc_final: 0.7155 (tt) REVERT: W 11 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7676 (mp) REVERT: X 11 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7904 (mt) REVERT: X 46 PHE cc_start: 0.4926 (m-10) cc_final: 0.4699 (m-10) REVERT: Y 11 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7715 (mp) REVERT: Y 16 MET cc_start: 0.8195 (mmp) cc_final: 0.7563 (mmt) REVERT: Y 146 PHE cc_start: 0.6323 (t80) cc_final: 0.6119 (t80) REVERT: Z 86 ILE cc_start: 0.8541 (mp) cc_final: 0.8303 (mp) REVERT: AA 22 MET cc_start: 0.8521 (mtt) cc_final: 0.8233 (ttt) REVERT: AA 61 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6371 (mm) REVERT: AA 146 PHE cc_start: 0.6759 (t80) cc_final: 0.6359 (t80) REVERT: BA 46 PHE cc_start: 0.5314 (m-10) cc_final: 0.5067 (m-10) outliers start: 85 outliers final: 49 residues processed: 647 average time/residue: 0.4735 time to fit residues: 552.8199 Evaluate side-chains 601 residues out of total 5427 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 541 time to evaluate : 5.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain B residue 11 ILE Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 154 ASN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 114 HIS Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 154 ASN Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 61 ILE Chi-restraints excluded: chain I residue 120 ILE Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain K residue 11 ILE Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 22 MET Chi-restraints excluded: chain L residue 197 VAL Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 154 ASN Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain P residue 53 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 154 ASN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 120 ILE Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 53 THR Chi-restraints excluded: chain S residue 120 ILE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 222 ILE Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 120 ILE Chi-restraints excluded: chain X residue 11 ILE Chi-restraints excluded: chain X residue 53 THR Chi-restraints excluded: chain X residue 111 GLN Chi-restraints excluded: chain X residue 120 ILE Chi-restraints excluded: chain X residue 154 ASN Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Z residue 13 VAL Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain Z residue 120 ILE Chi-restraints excluded: chain Z residue 154 ASN Chi-restraints excluded: chain AA residue 11 ILE Chi-restraints excluded: chain AA residue 53 THR Chi-restraints excluded: chain AA residue 61 ILE Chi-restraints excluded: chain BA residue 16 MET Chi-restraints excluded: chain BA residue 120 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 567 random chunks: chunk 357 optimal weight: 3.9990 chunk 479 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 414 optimal weight: 0.2980 chunk 66 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 450 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 462 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 HIS ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 HIS ** BA 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.137753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.103626 restraints weight = 89307.905| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.80 r_work: 0.3784 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 49221 Z= 0.168 Angle : 0.528 8.407 66042 Z= 0.266 Chirality : 0.041 0.135 7290 Planarity : 0.003 0.033 8397 Dihedral : 3.874 18.084 6426 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.80 % Allowed : 25.94 % Favored : 72.26 % 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: -0.94 (0.11), residues: 5751 helix: 0.80 (0.20), residues: 594 sheet: -0.95 (0.11), residues: 2376 loop : -0.48 (0.12), residues: 2781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPAA 179 HIS 0.005 0.001 HIS G 114 PHE 0.020 0.001 PHEBA 146 TYR 0.009 0.001 TYR T 52 ARG 0.006 0.000 ARG O 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11721.94 seconds wall clock time: 212 minutes 37.83 seconds (12757.83 seconds total)